chr3-160712081-A-G

Variant names:

• chr3-160712081-A-G
• rs7624766

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 0.493 in 152,048 control chromosomes in the GnomAD database, including 19,955 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 0.49 (19955 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.199
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.7 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: 0.493 AC: 74942 AN: 151930 Hom.: 19918 Cov.: 32

Gnomad AFR AF: 0.706

Gnomad AMI AF: 0.363

Gnomad AMR AF: 0.440

Gnomad ASJ AF: 0.337

Gnomad EAS AF: 0.610

Gnomad SAS AF: 0.366

Gnomad FIN AF: 0.386

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.404

Gnomad OTH AF: 0.440

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

GnomAD4 genome AF: 0.493 AC: 75032 AN: 152048 Hom.: 19955 Cov.: 32 AF XY: 0.489 AC XY: 36369 AN XY: 74324

African (AFR) AF: 0.707 AC: 29321 AN: 41498

American (AMR) AF: 0.439 AC: 6706 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.337 AC: 1169 AN: 3468

East Asian (EAS) AF: 0.611 AC: 3160 AN: 5176

South Asian (SAS) AF: 0.364 AC: 1752 AN: 4814

European-Finnish (FIN) AF: 0.386 AC: 4078 AN: 10558

Middle Eastern (MID) AF: 0.381 AC: 112 AN: 294

European-Non Finnish (NFE) AF: 0.404 AC: 27464 AN: 67944

Other (OTH) AF: 0.446 AC: 940 AN: 2108

Alfa AF: 0.435 Hom.: 48552

Bravo AF: 0.508

Asia WGS AF: 0.490 AC: 1702 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.3
DANN	Benign	0.62
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs7624766; hg19: chr3-160429869;