rs3916966

Variant names:

• chr13-105458546-C-A
• rs3916966

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 0.621 in 151,210 control chromosomes in the GnomAD database, including 29,451 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 0.62 (29451 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.77
• Publications: 14 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.694 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: 0.621 AC: 93861 AN: 151088 Hom.: 29424 Cov.: 28

Gnomad AFR AF: 0.701

Gnomad AMI AF: 0.590

Gnomad AMR AF: 0.586

Gnomad ASJ AF: 0.634

Gnomad EAS AF: 0.371

Gnomad SAS AF: 0.553

Gnomad FIN AF: 0.561

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.613

Gnomad OTH AF: 0.627

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

GnomAD4 genome AF: 0.621 AC: 93935 AN: 151210 Hom.: 29451 Cov.: 28 AF XY: 0.615 AC XY: 45372 AN XY: 73798

African (AFR) AF: 0.701 AC: 28871 AN: 41176

American (AMR) AF: 0.585 AC: 8882 AN: 15170

Ashkenazi Jewish (ASJ) AF: 0.634 AC: 2200 AN: 3468

East Asian (EAS) AF: 0.370 AC: 1872 AN: 5062

South Asian (SAS) AF: 0.554 AC: 2649 AN: 4784

European-Finnish (FIN) AF: 0.561 AC: 5857 AN: 10446

Middle Eastern (MID) AF: 0.634 AC: 185 AN: 292

European-Non Finnish (NFE) AF: 0.613 AC: 41574 AN: 67816

Other (OTH) AF: 0.627 AC: 1313 AN: 2094

Alfa AF: 0.617 Hom.: 88124

Bravo AF: 0.628

Asia WGS AF: 0.513 AC: 1786 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.031
DANN	Benign	0.38
PhyloP100		-2.8

Splicing

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

Other links and lift over

dbSNP: rs3916966; hg19: chr13-106110895;