rs16961766

chr13-103247149-C-Achr13-103247149-C-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.0531 in 152,284 control chromosomes in the GnomAD database, including 410 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 0.053 (410 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.688

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.37).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.115 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: 0.0531 AC: 8073 AN: 152166 Hom.: 409 Cov.: 32

Gnomad AFR AF: 0.118

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0616

Gnomad ASJ AF: 0.0265

Gnomad EAS AF: 0.103

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.0266

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0109

Gnomad OTH AF: 0.0478

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

GnomAD4 genome AF: 0.0531 AC: 8081 AN: 152284 Hom.: 410 Cov.: 32 AF XY: 0.0549 AC XY: 4087 AN XY: 74464

Gnomad4 AFR AF: 0.118

Gnomad4 AMR AF: 0.0615

Gnomad4 ASJ AF: 0.0265

Gnomad4 EAS AF: 0.103

Gnomad4 SAS AF: 0.101

Gnomad4 FIN AF: 0.0266

Gnomad4 NFE AF: 0.0109

Gnomad4 OTH AF: 0.0473

Alfa AF: 0.0196 Hom.: 126

Bravo AF: 0.0570

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.37
Cadd	Benign	13
Dann	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16961766; hg19: chr13-103899499;