rs11716921

Positions:

• chr3-17134100-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 0.134 in 152,188 control chromosomes in the GnomAD database, including 1,565 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 0.13 (1565 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.236

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.206 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: 0.134 AC: 20382 AN: 152070 Hom.: 1563 Cov.: 33

Gnomad AFR AF: 0.210

Gnomad AMI AF: 0.201

Gnomad AMR AF: 0.151

Gnomad ASJ AF: 0.0749

Gnomad EAS AF: 0.0993

Gnomad SAS AF: 0.0993

Gnomad FIN AF: 0.0559

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.103

Gnomad OTH AF: 0.134

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

GnomAD4 genome AF: 0.134 AC: 20398 AN: 152188 Hom.: 1565 Cov.: 33 AF XY: 0.133 AC XY: 9869 AN XY: 74414

Gnomad4 AFR AF: 0.210

Gnomad4 AMR AF: 0.151

Gnomad4 ASJ AF: 0.0749

Gnomad4 EAS AF: 0.0992

Gnomad4 SAS AF: 0.0996

Gnomad4 FIN AF: 0.0559

Gnomad4 NFE AF: 0.103

Gnomad4 OTH AF: 0.133

Alfa AF: 0.110 Hom.: 922

Bravo AF: 0.145

Asia WGS AF: 0.119 AC: 414 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.1
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11716921; hg19: chr3-17175592;