chr3-148641937-C-G

Variant names:

• chr3-148641937-C-G
• rs9862062

Variant summary

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

The variant allele was found at a frequency of 0.553 in 151,936 control chromosomes in the GnomAD database, including 24,681 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 0.55 (24681 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.204
• Publications: 5 publications found

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 (EAS) allele frequency at 95% confidence interval = 0.782 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.553 AC: 83911 AN: 151818 Hom.: 24662 Cov.: 31

Gnomad AFR AF: 0.360

Gnomad AMI AF: 0.499

Gnomad AMR AF: 0.689

Gnomad ASJ AF: 0.498

Gnomad EAS AF: 0.802

Gnomad SAS AF: 0.534

Gnomad FIN AF: 0.693

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.604

Gnomad OTH AF: 0.558

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

GnomAD4 genome AF: 0.553 AC: 83970 AN: 151936 Hom.: 24681 Cov.: 31 AF XY: 0.559 AC XY: 41517 AN XY: 74250

African (AFR) AF: 0.360 AC: 14897 AN: 41424

American (AMR) AF: 0.690 AC: 10524 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.498 AC: 1729 AN: 3470

East Asian (EAS) AF: 0.802 AC: 4119 AN: 5136

South Asian (SAS) AF: 0.536 AC: 2577 AN: 4810

European-Finnish (FIN) AF: 0.693 AC: 7318 AN: 10560

Middle Eastern (MID) AF: 0.449 AC: 132 AN: 294

European-Non Finnish (NFE) AF: 0.604 AC: 41048 AN: 67962

Other (OTH) AF: 0.555 AC: 1171 AN: 2110

Alfa AF: 0.561 Hom.: 3004

Bravo AF: 0.551

Asia WGS AF: 0.647 AC: 2247 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	1.5
DANN	Benign	0.48
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs9862062; hg19: chr3-148359724;