rs16961281

Positions:

• chr13-103066474-G-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 0.0749 in 459,014 control chromosomes in the GnomAD database, including 1,429 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 0.081 (553 hom., cov: 32)
  • Exomes 𝑓: 0.072 (876 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.974

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.6).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.111 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0807 AC: 12278 AN: 152132 Hom.: 550 Cov.: 32

Gnomad AFR AF: 0.114

Gnomad AMI AF: 0.0253

Gnomad AMR AF: 0.0571

Gnomad ASJ AF: 0.117

Gnomad EAS AF: 0.0634

Gnomad SAS AF: 0.0453

Gnomad FIN AF: 0.106

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0646

Gnomad OTH AF: 0.0789

GnomAD4 exome AF: 0.0720 AC: 22089 AN: 306764 Hom.: 876 Cov.: 4 AF XY: 0.0715 AC XY: 11178 AN XY: 156282

Gnomad4 AFR exome AF: 0.121

Gnomad4 AMR exome AF: 0.0490

Gnomad4 ASJ exome AF: 0.118

Gnomad4 EAS exome AF: 0.0571

Gnomad4 SAS exome AF: 0.0581

Gnomad4 FIN exome AF: 0.101

Gnomad4 NFE exome AF: 0.0671

Gnomad4 OTH exome AF: 0.0810

GnomAD4 genome AF: 0.0807 AC: 12294 AN: 152250 Hom.: 553 Cov.: 32 AF XY: 0.0818 AC XY: 6087 AN XY: 74428

Gnomad4 AFR AF: 0.114

Gnomad4 AMR AF: 0.0569

Gnomad4 ASJ AF: 0.117

Gnomad4 EAS AF: 0.0637

Gnomad4 SAS AF: 0.0456

Gnomad4 FIN AF: 0.106

Gnomad4 NFE AF: 0.0646

Gnomad4 OTH AF: 0.0785

Alfa AF: 0.0668 Hom.: 583

Bravo AF: 0.0784

Asia WGS AF: 0.0580 AC: 203 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	3.2
DANN	Benign	0.67

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs16961281; hg19: chr13-103718824;