chr3-103612639-G-A

Variant names:

• chr3-103612639-G-A
• rs9820695

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 0.426 in 152,004 control chromosomes in the GnomAD database, including 15,447 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 0.43 (15447 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.161
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.637 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.425 AC: 64596 AN: 151886 Hom.: 15395 Cov.: 32

Gnomad AFR AF: 0.643

Gnomad AMI AF: 0.224

Gnomad AMR AF: 0.451

Gnomad ASJ AF: 0.351

Gnomad EAS AF: 0.492

Gnomad SAS AF: 0.476

Gnomad FIN AF: 0.375

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.292

Gnomad OTH AF: 0.431

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

GnomAD4 genome AF: 0.426 AC: 64715 AN: 152004 Hom.: 15447 Cov.: 32 AF XY: 0.434 AC XY: 32217 AN XY: 74296

African (AFR) AF: 0.643 AC: 26670 AN: 41460

American (AMR) AF: 0.451 AC: 6887 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.351 AC: 1218 AN: 3470

East Asian (EAS) AF: 0.491 AC: 2532 AN: 5154

South Asian (SAS) AF: 0.478 AC: 2305 AN: 4818

European-Finnish (FIN) AF: 0.375 AC: 3968 AN: 10574

Middle Eastern (MID) AF: 0.493 AC: 145 AN: 294

European-Non Finnish (NFE) AF: 0.292 AC: 19864 AN: 67958

Other (OTH) AF: 0.437 AC: 922 AN: 2112

Alfa AF: 0.355 Hom.: 23936

Bravo AF: 0.441

Asia WGS AF: 0.544 AC: 1890 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.1
DANN	Benign	0.16
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs9820695; hg19: chr3-103331483;