dbSNP rs57344541: AHCY:c.-34C>T (chr20-34303304-G-A) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2

The NM_000687.4(AHCY):c.-34C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0106 in 1,551,714 control chromosomes in the GnomAD database, including 92 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

Frequency

Genomes: 𝑓 0.0079 ( 11 hom., cov: 34)

Exomes 𝑓: 0.011 ( 81 hom. )

Consequence

AHCY
NM_000687.4 5_prime_UTR

Scores

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:1B:2

Conservation

PhyloP100: -0.564

Publications

4 publications found

Variant links:

Genes affected

AHCY (HGNC:343): (adenosylhomocysteinase) S-adenosylhomocysteine hydrolase belongs to the adenosylhomocysteinase family. It catalyzes the reversible hydrolysis of S-adenosylhomocysteine (AdoHcy) to adenosine (Ado) and L-homocysteine (Hcy). Thus, it regulates the intracellular S-adenosylhomocysteine (SAH) concentration thought to be important for transmethylation reactions. Deficiency in this protein is one of the different causes of hypermethioninemia. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jun 2009]

AHCY Gene-Disease associations (from GenCC):

hypermethioninemia with deficiency of S-adenosylhomocysteine hydrolase
Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: ClinGen, Labcorp Genetics (formerly Invitae), Orphanet

AHCY links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.67).

BP6

Variant 20-34303304-G-A is Benign according to our data. Variant chr20-34303304-G-A is described in ClinVar as Conflicting_classifications_of_pathogenicity. ClinVar VariationId is 218468.

BS1

Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.00795 (1211/152362) while in subpopulation NFE AF = 0.0127 (864/68030). AF 95% confidence interval is 0.012. There are 11 homozygotes in GnomAd4. There are 589 alleles in the male GnomAd4 subpopulation. Median coverage is 34. This position passed quality control check.

BS2

High Homozygotes in GnomAd4 at 11 AR gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000687.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
AHCY	NM_000687.4	MANE Select	c.-34C>T	5_prime_UTR	Exon 1 of 10	NP_000678.1	A0A384MTQ3
AHCY	NM_001362750.2		c.-34C>T	5_prime_UTR	Exon 1 of 11	NP_001349679.1	A0A384MTQ3
AHCY	NM_001161766.2		c.-56-7719C>T	intron	N/A	NP_001155238.1	P23526-2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
AHCY	ENST00000217426.7	TSL:1 MANE Select	c.-34C>T	5_prime_UTR	Exon 1 of 10	ENSP00000217426.2	P23526-1
AHCY	ENST00000538132.1	TSL:2	c.-56-7719C>T	intron	N/A	ENSP00000442820.1	P23526-2
AHCY	ENST00000480653.5	TSL:2	n.14C>T	non_coding_transcript_exon	Exon 1 of 9

Frequencies

GnomAD3 genomes

AF:

0.00795

AC:

1211

AN:

152244

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00190

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00432

Gnomad ASJ

AF:

0.0104

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.00207

Gnomad FIN

AF:

0.0136

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0127

Gnomad OTH

AF:

0.00525

GnomAD2 exomes

AF:

0.00771

AC:

1205

AN:

156280

AF XY:

0.00782

show subpopulations

Gnomad AFR exome

AF:

0.00104

Gnomad AMR exome

AF:

0.00400

Gnomad ASJ exome

AF:

0.00856

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.0146

Gnomad NFE exome

AF:

0.0120

Gnomad OTH exome

AF:

0.00747

GnomAD4 exome

AF:

0.0109

AC:

15209

AN:

1399352

Hom.:

Cov.:

AF XY:

0.0107

AC XY:

7391

AN XY:

690196

show subpopulations

African (AFR)

AF:

0.00158

AC:

AN:

31596

American (AMR)

AF:

0.00372

AC:

133

AN:

35710

Ashkenazi Jewish (ASJ)

AF:

0.00914

AC:

230

AN:

25176

East Asian (EAS)

AF:

0.00

AC:

AN:

35746

South Asian (SAS)

AF:

0.00196

AC:

155

AN:

79232

European-Finnish (FIN)

AF:

0.0137

AC:

674

AN:

49262

Middle Eastern (MID)

AF:

0.00351

AC:

AN:

5698

European-Non Finnish (NFE)

AF:

0.0124

AC:

13372

AN:

1078930

Other (OTH)

AF:

0.00991

AC:

575

AN:

58002

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.458

Heterozygous variant carriers

779

1557

2336

3114

3893

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

502

1004

1506

2008

2510

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.00795

AC:

1211

AN:

152362

Hom.:

Cov.:

AF XY:

0.00791

AC XY:

589

AN XY:

74500

show subpopulations

African (AFR)

AF:

0.00190

AC:

AN:

41594

American (AMR)

AF:

0.00431

AC:

AN:

15314

Ashkenazi Jewish (ASJ)

AF:

0.0104

AC:

AN:

3468

East Asian (EAS)

AF:

0.000193

AC:

AN:

5176

South Asian (SAS)

AF:

0.00207

AC:

AN:

4832

European-Finnish (FIN)

AF:

0.0136

AC:

144

AN:

10626

Middle Eastern (MID)

AF:

0.00

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0127

AC:

864

AN:

68030

Other (OTH)

AF:

0.00520

AC:

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.497

Heterozygous variant carriers

129

193

258

322

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

100

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0113

Hom.:

Bravo

AF:

0.00686

Asia WGS

AF:

0.000289

AC:

AN:

3478

ClinVar

ClinVar submissions

Significance:Conflicting classifications of pathogenicity

Revision:criteria provided, conflicting classifications

View on ClinVar

Pathogenic

VUS

Benign

Condition

Hypermethioninemia with deficiency of S-adenosylhomocysteine hydrolase (2)

not specified (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.67

CADD

Benign

(source)

DANN

Benign

0.91

PhyloP100

-0.56

PromoterAI

0.25

Neutral

(source)

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

2.1

Mutation Taster

=100/0

polymorphism

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over