rs11716921

Variant names:

• chr3-17134100-T-G
• rs11716921

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.210 AC: 8716 AN: 41476

American (AMR) AF: 0.151 AC: 2314 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0749 AC: 260 AN: 3472

East Asian (EAS) AF: 0.0992 AC: 514 AN: 5182

South Asian (SAS) AF: 0.0996 AC: 481 AN: 4830

European-Finnish (FIN) AF: 0.0559 AC: 593 AN: 10610

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.103 AC: 7022 AN: 68008

Other (OTH) AF: 0.133 AC: 281 AN: 2108

Alfa AF: 0.116 Hom.: 1298

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
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs11716921; hg19: chr3-17175592;