rs2071522

chr11-116826822-T-Cchr11-116826822-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 0.528 in 151,990 control chromosomes in the GnomAD database, including 22,602 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 0.53 (22602 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0570

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.626 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: 0.528 AC: 80254 AN: 151872 Hom.: 22604 Cov.: 32

Gnomad AFR AF: 0.315

Gnomad AMI AF: 0.678

Gnomad AMR AF: 0.569

Gnomad ASJ AF: 0.560

Gnomad EAS AF: 0.614

Gnomad SAS AF: 0.494

Gnomad FIN AF: 0.588

Gnomad MID AF: 0.564

Gnomad NFE AF: 0.631

Gnomad OTH AF: 0.553

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

GnomAD4 genome AF: 0.528 AC: 80273 AN: 151990 Hom.: 22602 Cov.: 32 AF XY: 0.523 AC XY: 38875 AN XY: 74266

Gnomad4 AFR AF: 0.315

Gnomad4 AMR AF: 0.569

Gnomad4 ASJ AF: 0.560

Gnomad4 EAS AF: 0.615

Gnomad4 SAS AF: 0.493

Gnomad4 FIN AF: 0.588

Gnomad4 NFE AF: 0.631

Gnomad4 OTH AF: 0.554

Alfa AF: 0.569 Hom.: 3198

Bravo AF: 0.526

Asia WGS AF: 0.538 AC: 1875 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	5.4
Dann	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2071522; hg19: chr11-116697538;