rs3916966

chr13-105458546-C-A

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 0.621 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.701

Gnomad4 AMR AF: 0.585

Gnomad4 ASJ AF: 0.634

Gnomad4 EAS AF: 0.370

Gnomad4 SAS AF: 0.554

Gnomad4 FIN AF: 0.561

Gnomad4 NFE AF: 0.613

Gnomad4 OTH AF: 0.627

Alfa AF: 0.614 Hom.: 54636

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3916966; hg19: chr13-106110895;