rs402675

Positions:

• chr3-1581709-T-A
• chr3-1581709-T-C

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 0.371 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

ACMG classification

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.224

Gnomad4 AMR AF: 0.283

Gnomad4 ASJ AF: 0.384

Gnomad4 EAS AF: 0.0874

Gnomad4 SAS AF: 0.362

Gnomad4 FIN AF: 0.489

Gnomad4 NFE AF: 0.483

Gnomad4 OTH AF: 0.347

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs402675; hg19: chr3-1623393;