rs2097171

Positions:

• chr11-81612429-C-T

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;