rs2071522

Variant names:

• chr11-116826822-T-C
• rs2071522

Your query was ambiguous. Multiple possible variants found:

• chr11-116826822-T-C
• chr11-116826822-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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;