dbSNP rs9356970: CMAHP:n.519-2432C>T (chr6-25257738-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000413898.3(CMAHP):n.519-2432C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.286 in 152,202 control chromosomes in the GnomAD database, including 7,886 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 0.29 ( 7886 hom., cov: 33)

Consequence

CMAHP
ENST00000413898.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.323

Publications

1 publications found

Variant links:

Genes affected

CMAHP (HGNC:):

CMAHP links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.596 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101928663	NR_110862.1 link	n.514-2432C>T		intron_variant	Intron 2 of 3
LOC101928663	NR_110863.1 link	n.513+2610C>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
CMAHP	ENST00000413898.3 link	n.519-2432C>T	intron_variant	Intron 2 of 3	1
CMAHP	ENST00000643481.1 link	n.517-2432C>T	intron_variant	Intron 2 of 5
CMAHP	ENST00000643656.2 link	n.267-2432C>T	intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes

AF:

0.286

AC:

43473

AN:

152086

Hom.:

7882

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0717

Gnomad AMI

AF:

0.439

Gnomad AMR

AF:

0.331

Gnomad ASJ

AF:

0.320

Gnomad EAS

AF:

0.612

Gnomad SAS

AF:

0.461

Gnomad FIN

AF:

0.454

Gnomad MID

AF:

0.234

Gnomad NFE

AF:

0.340

Gnomad OTH

AF:

0.262

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.286

AC:

43477

AN:

152202

Hom.:

7886

Cov.:

AF XY:

0.298

AC XY:

22158

AN XY:

74412

show subpopulations

African (AFR)

AF:

0.0715

AC:

2970

AN:

41554

American (AMR)

AF:

0.332

AC:

5070

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.320

AC:

1110

AN:

3472

East Asian (EAS)

AF:

0.614

AC:

3176

AN:

5174

South Asian (SAS)

AF:

0.460

AC:

2218

AN:

4826

European-Finnish (FIN)

AF:

0.454

AC:

4807

AN:

10582

Middle Eastern (MID)

AF:

0.228

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.340

AC:

23100

AN:

67986

Other (OTH)

AF:

0.264

AC:

559

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1485

2969

4454

5938

7423

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

450

900

1350

1800

2250

<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:

0.300

Hom.:

9612

Bravo

AF:

0.262

Asia WGS

AF:

0.467

AC:

1622

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

1.3

(source)

DANN

Benign

0.75

PhyloP100

-0.32

Splicing

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over