3-103660982-G-A

Variant names:

• chr3-103660982-G-A
• rs10511216

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 0.0942 in 151,898 control chromosomes in the GnomAD database, including 852 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 0.094 (852 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.839
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.251 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: 0.0942 AC: 14292 AN: 151780 Hom.: 848 Cov.: 32

Gnomad AFR AF: 0.0785

Gnomad AMI AF: 0.0844

Gnomad AMR AF: 0.0958

Gnomad ASJ AF: 0.131

Gnomad EAS AF: 0.262

Gnomad SAS AF: 0.179

Gnomad FIN AF: 0.0166

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.0940

Gnomad OTH AF: 0.112

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

GnomAD4 genome AF: 0.0942 AC: 14308 AN: 151898 Hom.: 852 Cov.: 32 AF XY: 0.0932 AC XY: 6918 AN XY: 74238

African (AFR) AF: 0.0786 AC: 3260 AN: 41490

American (AMR) AF: 0.0957 AC: 1457 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.131 AC: 454 AN: 3466

East Asian (EAS) AF: 0.262 AC: 1336 AN: 5092

South Asian (SAS) AF: 0.180 AC: 869 AN: 4822

European-Finnish (FIN) AF: 0.0166 AC: 176 AN: 10610

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.0940 AC: 6383 AN: 67870

Other (OTH) AF: 0.111 AC: 235 AN: 2110

Alfa AF: 0.0873 Hom.: 127

Bravo AF: 0.0999

Asia WGS AF: 0.218 AC: 758 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	9.2
DANN	Benign	0.52
PhyloP100		0.84

Splicing

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

Other links and lift over

dbSNP: rs10511216; hg19: chr3-103379826;