3-69579952-T-C

Variant names:

• chr3-69579952-T-C
• rs288503

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 0.646 in 151,920 control chromosomes in the GnomAD database, including 32,440 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 0.65 (32440 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.224
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.54).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.825 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: 0.646 AC: 98075 AN: 151804 Hom.: 32407 Cov.: 31

Gnomad AFR AF: 0.735

Gnomad AMI AF: 0.506

Gnomad AMR AF: 0.702

Gnomad ASJ AF: 0.597

Gnomad EAS AF: 0.846

Gnomad SAS AF: 0.751

Gnomad FIN AF: 0.506

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.584

Gnomad OTH AF: 0.623

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

GnomAD4 genome AF: 0.646 AC: 98153 AN: 151920 Hom.: 32440 Cov.: 31 AF XY: 0.648 AC XY: 48077 AN XY: 74224

African (AFR) AF: 0.735 AC: 30459 AN: 41430

American (AMR) AF: 0.702 AC: 10724 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.597 AC: 2073 AN: 3470

East Asian (EAS) AF: 0.846 AC: 4357 AN: 5152

South Asian (SAS) AF: 0.751 AC: 3617 AN: 4818

European-Finnish (FIN) AF: 0.506 AC: 5329 AN: 10528

Middle Eastern (MID) AF: 0.476 AC: 140 AN: 294

European-Non Finnish (NFE) AF: 0.584 AC: 39697 AN: 67950

Other (OTH) AF: 0.617 AC: 1299 AN: 2106

Alfa AF: 0.615 Hom.: 16549

Bravo AF: 0.662

Asia WGS AF: 0.777 AC: 2701 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
CADD	Benign	8.8
DANN	Benign	0.46
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs288503; hg19: chr3-69629103;