3-69574037-G-T

Variant names:

• chr3-69574037-G-T
• rs7647307

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 0.504 in 151,506 control chromosomes in the GnomAD database, including 19,617 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 0.50 (19617 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0710
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.598 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: 0.504 AC: 76289 AN: 151390 Hom.: 19607 Cov.: 32

Gnomad AFR AF: 0.425

Gnomad AMI AF: 0.457

Gnomad AMR AF: 0.607

Gnomad ASJ AF: 0.490

Gnomad EAS AF: 0.585

Gnomad SAS AF: 0.546

Gnomad FIN AF: 0.483

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.525

Gnomad OTH AF: 0.491

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

GnomAD4 genome AF: 0.504 AC: 76326 AN: 151506 Hom.: 19617 Cov.: 32 AF XY: 0.506 AC XY: 37436 AN XY: 74018

African (AFR) AF: 0.425 AC: 17553 AN: 41344

American (AMR) AF: 0.608 AC: 9239 AN: 15196

Ashkenazi Jewish (ASJ) AF: 0.490 AC: 1698 AN: 3466

East Asian (EAS) AF: 0.584 AC: 3003 AN: 5142

South Asian (SAS) AF: 0.545 AC: 2622 AN: 4808

European-Finnish (FIN) AF: 0.483 AC: 5069 AN: 10484

Middle Eastern (MID) AF: 0.363 AC: 106 AN: 292

European-Non Finnish (NFE) AF: 0.525 AC: 35599 AN: 67766

Other (OTH) AF: 0.487 AC: 1023 AN: 2102

Alfa AF: 0.514 Hom.: 42829

Bravo AF: 0.511

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.6
DANN	Benign	0.50
PhyloP100		0.071

Splicing

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

Other links and lift over

dbSNP: rs7647307; hg19: chr3-69623188;