rs2113334

Positions:

• chr16-13882499-T-C
• chr16-13882499-T-G

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 0.633 in 152,110 control chromosomes in the GnomAD database, including 32,953 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 0.63 (32953 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.766

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.759 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: 0.633 AC: 96199 AN: 151992 Hom.: 32957 Cov.: 31

Gnomad AFR AF: 0.374

Gnomad AMI AF: 0.689

Gnomad AMR AF: 0.745

Gnomad ASJ AF: 0.770

Gnomad EAS AF: 0.349

Gnomad SAS AF: 0.533

Gnomad FIN AF: 0.765

Gnomad MID AF: 0.737

Gnomad NFE AF: 0.764

Gnomad OTH AF: 0.651

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

GnomAD4 genome AF: 0.633 AC: 96225 AN: 152110 Hom.: 32953 Cov.: 31 AF XY: 0.632 AC XY: 46995 AN XY: 74346

Gnomad4 AFR AF: 0.374

Gnomad4 AMR AF: 0.745

Gnomad4 ASJ AF: 0.770

Gnomad4 EAS AF: 0.349

Gnomad4 SAS AF: 0.531

Gnomad4 FIN AF: 0.765

Gnomad4 NFE AF: 0.764

Gnomad4 OTH AF: 0.654

Alfa AF: 0.736 Hom.: 90404

Bravo AF: 0.620

Asia WGS AF: 0.411 AC: 1433 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	10
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2113334; hg19: chr16-13976356;