11-21628265-C-T

Variant names:

• chr11-21628265-C-T
• rs7931276

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 0.161 in 152,154 control chromosomes in the GnomAD database, including 2,077 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 0.16 (2077 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.326
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.188 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: 0.161 AC: 24436 AN: 152036 Hom.: 2074 Cov.: 32

Gnomad AFR AF: 0.153

Gnomad AMI AF: 0.321

Gnomad AMR AF: 0.194

Gnomad ASJ AF: 0.104

Gnomad EAS AF: 0.111

Gnomad SAS AF: 0.122

Gnomad FIN AF: 0.0995

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.175

Gnomad OTH AF: 0.147

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

GnomAD4 genome AF: 0.161 AC: 24447 AN: 152154 Hom.: 2077 Cov.: 32 AF XY: 0.157 AC XY: 11704 AN XY: 74372

African (AFR) AF: 0.153 AC: 6356 AN: 41508

American (AMR) AF: 0.194 AC: 2961 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.104 AC: 361 AN: 3464

East Asian (EAS) AF: 0.111 AC: 572 AN: 5170

South Asian (SAS) AF: 0.122 AC: 590 AN: 4824

European-Finnish (FIN) AF: 0.0995 AC: 1055 AN: 10598

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.175 AC: 11906 AN: 67996

Other (OTH) AF: 0.146 AC: 307 AN: 2108

Alfa AF: 0.166 Hom.: 3663

Bravo AF: 0.168

Asia WGS AF: 0.108 AC: 377 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.50
DANN	Benign	0.62
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs7931276; hg19: chr11-21649811;