13-103247149-C-A

Variant names:

• chr13-103247149-C-A
• rs16961766

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;