rs402675

Variant names:

• chr3-1581709-T-A
• rs402675

Your query was ambiguous. Multiple possible variants found:

• chr3-1581709-T-A
• chr3-1581709-T-C

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 0.371 in 152,004 control chromosomes in the GnomAD database, including 11,788 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 0.37 (11788 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.136
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.479 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: 0.371 AC: 56422 AN: 151884 Hom.: 11791 Cov.: 32

Gnomad AFR AF: 0.224

Gnomad AMI AF: 0.475

Gnomad AMR AF: 0.284

Gnomad ASJ AF: 0.384

Gnomad EAS AF: 0.0874

Gnomad SAS AF: 0.363

Gnomad FIN AF: 0.489

Gnomad MID AF: 0.318

Gnomad NFE AF: 0.483

Gnomad OTH AF: 0.352

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

GnomAD4 genome AF: 0.371 AC: 56417 AN: 152004 Hom.: 11788 Cov.: 32 AF XY: 0.367 AC XY: 27296 AN XY: 74314

African (AFR) AF: 0.224 AC: 9304 AN: 41478

American (AMR) AF: 0.283 AC: 4326 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.384 AC: 1334 AN: 3472

East Asian (EAS) AF: 0.0874 AC: 451 AN: 5162

South Asian (SAS) AF: 0.362 AC: 1747 AN: 4820

European-Finnish (FIN) AF: 0.489 AC: 5159 AN: 10548

Middle Eastern (MID) AF: 0.305 AC: 89 AN: 292

European-Non Finnish (NFE) AF: 0.483 AC: 32844 AN: 67934

Other (OTH) AF: 0.347 AC: 730 AN: 2104

Alfa AF: 0.426 Hom.: 1829

Bravo AF: 0.349

Asia WGS AF: 0.200 AC: 696 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	3.4
DANN	Benign	0.42
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs402675; hg19: chr3-1623393;