3-69559956-C-T

Variant names:

• chr3-69559956-C-T
• rs1498853

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 0.731 in 152,076 control chromosomes in the GnomAD database, including 41,553 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 0.73 (41553 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.917 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: 0.731 AC: 111006 AN: 151958 Hom.: 41511 Cov.: 31

Gnomad AFR AF: 0.870

Gnomad AMI AF: 0.574

Gnomad AMR AF: 0.762

Gnomad ASJ AF: 0.659

Gnomad EAS AF: 0.939

Gnomad SAS AF: 0.764

Gnomad FIN AF: 0.617

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.646

Gnomad OTH AF: 0.696

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

GnomAD4 genome AF: 0.731 AC: 111099 AN: 152076 Hom.: 41553 Cov.: 31 AF XY: 0.732 AC XY: 54378 AN XY: 74318

African (AFR) AF: 0.870 AC: 36109 AN: 41516

American (AMR) AF: 0.763 AC: 11655 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.659 AC: 2287 AN: 3470

East Asian (EAS) AF: 0.939 AC: 4847 AN: 5164

South Asian (SAS) AF: 0.763 AC: 3675 AN: 4818

European-Finnish (FIN) AF: 0.617 AC: 6510 AN: 10544

Middle Eastern (MID) AF: 0.520 AC: 153 AN: 294

European-Non Finnish (NFE) AF: 0.646 AC: 43885 AN: 67966

Other (OTH) AF: 0.690 AC: 1456 AN: 2110

Alfa AF: 0.672 Hom.: 146080

Bravo AF: 0.747

Asia WGS AF: 0.834 AC: 2903 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.19
DANN	Benign	0.40
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs1498853; hg19: chr3-69609107;