rs2097171

Variant names:

• chr11-81612429-C-T
• rs2097171

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 0.482 in 152,076 control chromosomes in the GnomAD database, including 18,736 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 0.48 (18736 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.281

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.659 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: 0.483 AC: 73352 AN: 151958 Hom.: 18731 Cov.: 33

Gnomad AFR AF: 0.309

Gnomad AMI AF: 0.323

Gnomad AMR AF: 0.534

Gnomad ASJ AF: 0.597

Gnomad EAS AF: 0.477

Gnomad SAS AF: 0.679

Gnomad FIN AF: 0.626

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.535

Gnomad OTH AF: 0.527

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

GnomAD4 genome AF: 0.482 AC: 73362 AN: 152076 Hom.: 18736 Cov.: 33 AF XY: 0.490 AC XY: 36456 AN XY: 74350

Gnomad4 AFR AF: 0.308

Gnomad4 AMR AF: 0.534

Gnomad4 ASJ AF: 0.597

Gnomad4 EAS AF: 0.477

Gnomad4 SAS AF: 0.679

Gnomad4 FIN AF: 0.626

Gnomad4 NFE AF: 0.535

Gnomad4 OTH AF: 0.524

Alfa AF: 0.490 Hom.: 3551

Bravo AF: 0.468

Asia WGS AF: 0.563 AC: 1959 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	5.0
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2097171; hg19: chr11-81323471;