rs3916964

Variant names:

• chr13-105427084-G-A
• rs3916964

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 0.402 in 151,868 control chromosomes in the GnomAD database, including 12,585 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 0.40 (12585 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.624 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: 0.402 AC: 60933 AN: 151750 Hom.: 12573 Cov.: 32

Gnomad AFR AF: 0.344

Gnomad AMI AF: 0.284

Gnomad AMR AF: 0.474

Gnomad ASJ AF: 0.328

Gnomad EAS AF: 0.642

Gnomad SAS AF: 0.353

Gnomad FIN AF: 0.350

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.419

Gnomad OTH AF: 0.391

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

GnomAD4 genome AF: 0.402 AC: 60980 AN: 151868 Hom.: 12585 Cov.: 32 AF XY: 0.399 AC XY: 29631 AN XY: 74172

African (AFR) AF: 0.344 AC: 14264 AN: 41424

American (AMR) AF: 0.475 AC: 7249 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.328 AC: 1137 AN: 3464

East Asian (EAS) AF: 0.642 AC: 3301 AN: 5138

South Asian (SAS) AF: 0.352 AC: 1696 AN: 4824

European-Finnish (FIN) AF: 0.350 AC: 3681 AN: 10520

Middle Eastern (MID) AF: 0.347 AC: 102 AN: 294

European-Non Finnish (NFE) AF: 0.419 AC: 28463 AN: 67920

Other (OTH) AF: 0.393 AC: 829 AN: 2110

Alfa AF: 0.417 Hom.: 13060

Bravo AF: 0.411

Asia WGS AF: 0.473 AC: 1637 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.14
DANN	Benign	0.35
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs3916964; hg19: chr13-106079433;