chr3-69574037-G-T

Position:

• chr3-69574037-G-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.425

Gnomad4 AMR AF: 0.608

Gnomad4 ASJ AF: 0.490

Gnomad4 EAS AF: 0.584

Gnomad4 SAS AF: 0.545

Gnomad4 FIN AF: 0.483

Gnomad4 NFE AF: 0.525

Gnomad4 OTH AF: 0.487

Alfa AF: 0.517 Hom.: 29133

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7647307; hg19: chr3-69623188;