chr3-103684670-C-T

Variant names:

• chr3-103684670-C-T
• rs10511217

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 0.325 in 151,782 control chromosomes in the GnomAD database, including 8,656 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 0.32 (8656 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0510
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.52).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.435 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: 0.325 AC: 49219 AN: 151664 Hom.: 8616 Cov.: 32

Gnomad AFR AF: 0.440

Gnomad AMI AF: 0.143

Gnomad AMR AF: 0.373

Gnomad ASJ AF: 0.276

Gnomad EAS AF: 0.308

Gnomad SAS AF: 0.409

Gnomad FIN AF: 0.372

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.237

Gnomad OTH AF: 0.305

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

GnomAD4 genome AF: 0.325 AC: 49311 AN: 151782 Hom.: 8656 Cov.: 32 AF XY: 0.334 AC XY: 24800 AN XY: 74168

African (AFR) AF: 0.440 AC: 18225 AN: 41400

American (AMR) AF: 0.374 AC: 5685 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.276 AC: 956 AN: 3470

East Asian (EAS) AF: 0.307 AC: 1577 AN: 5134

South Asian (SAS) AF: 0.410 AC: 1980 AN: 4826

European-Finnish (FIN) AF: 0.372 AC: 3931 AN: 10558

Middle Eastern (MID) AF: 0.269 AC: 78 AN: 290

European-Non Finnish (NFE) AF: 0.237 AC: 16095 AN: 67876

Other (OTH) AF: 0.312 AC: 654 AN: 2098

Alfa AF: 0.268 Hom.: 15548

Bravo AF: 0.329

Asia WGS AF: 0.422 AC: 1466 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.52
CADD	Benign	5.6
DANN	Benign	0.63
PhyloP100		-0.051

Splicing

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

Other links and lift over

dbSNP: rs10511217; hg19: chr3-103403514;