3-171532079-G-T

Variant names:

• chr3-171532079-G-T
• rs260770

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 0.728 in 152,056 control chromosomes in the GnomAD database, including 41,364 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 (41364 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.21
• Publications: 1 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 = 0.875 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: 0.728 AC: 110622 AN: 151938 Hom.: 41314 Cov.: 31

Gnomad AFR AF: 0.883

Gnomad AMI AF: 0.673

Gnomad AMR AF: 0.650

Gnomad ASJ AF: 0.655

Gnomad EAS AF: 0.368

Gnomad SAS AF: 0.608

Gnomad FIN AF: 0.731

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.692

Gnomad OTH AF: 0.708

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

GnomAD4 genome AF: 0.728 AC: 110728 AN: 152056 Hom.: 41364 Cov.: 31 AF XY: 0.724 AC XY: 53828 AN XY: 74336

African (AFR) AF: 0.883 AC: 36620 AN: 41482

American (AMR) AF: 0.650 AC: 9943 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.655 AC: 2272 AN: 3470

East Asian (EAS) AF: 0.367 AC: 1899 AN: 5168

South Asian (SAS) AF: 0.608 AC: 2927 AN: 4812

European-Finnish (FIN) AF: 0.731 AC: 7721 AN: 10558

Middle Eastern (MID) AF: 0.731 AC: 215 AN: 294

European-Non Finnish (NFE) AF: 0.692 AC: 47033 AN: 67960

Other (OTH) AF: 0.704 AC: 1484 AN: 2108

Alfa AF: 0.722 Hom.: 4986

Bravo AF: 0.726

Asia WGS AF: 0.496 AC: 1726 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	1.0
DANN	Benign	0.45
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs260770; hg19: chr3-171249868;