chr3-101135338-C-G

Variant names:

• chr3-101135338-C-G
• rs1911573

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 0.683 in 151,778 control chromosomes in the GnomAD database, including 35,841 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 0.68 (35841 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.107
• Publications: 0 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 = 0.831 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: 0.683 AC: 103524 AN: 151660 Hom.: 35775 Cov.: 32

Gnomad AFR AF: 0.782

Gnomad AMI AF: 0.639

Gnomad AMR AF: 0.716

Gnomad ASJ AF: 0.572

Gnomad EAS AF: 0.852

Gnomad SAS AF: 0.641

Gnomad FIN AF: 0.656

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.616

Gnomad OTH AF: 0.661

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

GnomAD4 genome AF: 0.683 AC: 103650 AN: 151778 Hom.: 35841 Cov.: 32 AF XY: 0.687 AC XY: 50953 AN XY: 74154

African (AFR) AF: 0.782 AC: 32408 AN: 41428

American (AMR) AF: 0.716 AC: 10911 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.572 AC: 1984 AN: 3466

East Asian (EAS) AF: 0.852 AC: 4365 AN: 5122

South Asian (SAS) AF: 0.641 AC: 3086 AN: 4814

European-Finnish (FIN) AF: 0.656 AC: 6924 AN: 10556

Middle Eastern (MID) AF: 0.575 AC: 169 AN: 294

European-Non Finnish (NFE) AF: 0.616 AC: 41818 AN: 67836

Other (OTH) AF: 0.665 AC: 1405 AN: 2114

Alfa AF: 0.536 Hom.: 1478

Bravo AF: 0.690

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.1
DANN	Benign	0.34
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs1911573; hg19: chr3-100854182;