11-21655796-G-T

Variant names:

• chr11-21655796-G-T
• rs2051457

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 0.0736 in 151,892 control chromosomes in the GnomAD database, including 977 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 0.074 (977 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.174

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.195 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: 0.0735 AC: 11161 AN: 151774 Hom.: 977 Cov.: 32

Gnomad AFR AF: 0.199

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0644

Gnomad ASJ AF: 0.00462

Gnomad EAS AF: 0.146

Gnomad SAS AF: 0.107

Gnomad FIN AF: 0.0136

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.00592

Gnomad OTH AF: 0.0633

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

GnomAD4 genome AF: 0.0736 AC: 11177 AN: 151892 Hom.: 977 Cov.: 32 AF XY: 0.0755 AC XY: 5606 AN XY: 74230

Gnomad4 AFR AF: 0.199

Gnomad4 AMR AF: 0.0644

Gnomad4 ASJ AF: 0.00462

Gnomad4 EAS AF: 0.147

Gnomad4 SAS AF: 0.106

Gnomad4 FIN AF: 0.0136

Gnomad4 NFE AF: 0.00592

Gnomad4 OTH AF: 0.0636

Alfa AF: 0.0202 Hom.: 199

Bravo AF: 0.0824

Asia WGS AF: 0.129 AC: 446 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	5.4
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2051457; hg19: chr11-21677342;