7-129429137-G-A

Variant names:

• chr7-129429137-G-A
• rs1665105
• NM_015328.4:c.*2092G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_015328.4(AHCYL2):​c.*2092G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.456 in 152,022 control chromosomes in the GnomAD database, including 16,022 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.46 (16022 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: AHCYL2 NM_015328.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.43
• Publications: 11 publications found

Genes affected

AHCYL2 (HGNC:22204): (adenosylhomocysteinase like 2) The protein encoded by this gene acts as a homotetramer and may be involved in the conversion of S-adenosyl-L-homocysteine to L-homocysteine and adenosine. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jun 2011]

ENSG00000300026 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.486 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015328.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AHCYL2	NM_015328.4	MANE Select	c.*2092G>A		3_prime_UTR	Exon 17 of 17	NP_056143.1
	AHCYL2	NR_171671.1		n.4054G>A		non_coding_transcript_exon	Exon 18 of 18
	AHCYL2	NM_001130720.3		c.*2092G>A		3_prime_UTR	Exon 17 of 17	NP_001124192.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AHCYL2	ENST00000325006.8	TSL:1 MANE Select	c.*2092G>A		3_prime_UTR	Exon 17 of 17	ENSP00000315931.3
	AHCYL2	ENST00000446544.6	TSL:1	c.*2092G>A		3_prime_UTR	Exon 17 of 17	ENSP00000413639.2
	ENSG00000300026	ENST00000768233.1		n.207+4190C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.456 AC: 69318 AN: 151904 Hom.: 16014 Cov.: 32

Gnomad AFR AF: 0.482

Gnomad AMI AF: 0.488

Gnomad AMR AF: 0.495

Gnomad ASJ AF: 0.520

Gnomad EAS AF: 0.382

Gnomad SAS AF: 0.412

Gnomad FIN AF: 0.400

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.443

Gnomad OTH AF: 0.521

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.456 AC: 69357 AN: 152022 Hom.: 16022 Cov.: 32 AF XY: 0.454 AC XY: 33697 AN XY: 74304

African (AFR) AF: 0.482 AC: 19975 AN: 41454

American (AMR) AF: 0.496 AC: 7573 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.520 AC: 1807 AN: 3472

East Asian (EAS) AF: 0.381 AC: 1970 AN: 5168

South Asian (SAS) AF: 0.411 AC: 1981 AN: 4824

European-Finnish (FIN) AF: 0.400 AC: 4218 AN: 10542

Middle Eastern (MID) AF: 0.517 AC: 152 AN: 294

European-Non Finnish (NFE) AF: 0.443 AC: 30142 AN: 67970

Other (OTH) AF: 0.518 AC: 1095 AN: 2112

Alfa AF: 0.455 Hom.: 30981

Bravo AF: 0.464

Asia WGS AF: 0.432 AC: 1504 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.0040
DANN	Benign	0.45
PhyloP100		-2.4
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1665105; hg19: chr7-129068978;