rs2197040

Variant names:

• chr11-13161235-C-T
• rs2197040

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 0.172 in 152,120 control chromosomes in the GnomAD database, including 3,563 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 0.17 (3563 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.60

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.375 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: 0.172 AC: 26135 AN: 152002 Hom.: 3560 Cov.: 32

Gnomad AFR AF: 0.380

Gnomad AMI AF: 0.0351

Gnomad AMR AF: 0.113

Gnomad ASJ AF: 0.107

Gnomad EAS AF: 0.0922

Gnomad SAS AF: 0.112

Gnomad FIN AF: 0.0520

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.0930

Gnomad OTH AF: 0.154

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

GnomAD4 genome AF: 0.172 AC: 26157 AN: 152120 Hom.: 3563 Cov.: 32 AF XY: 0.167 AC XY: 12426 AN XY: 74402

Gnomad4 AFR AF: 0.380

Gnomad4 AMR AF: 0.113

Gnomad4 ASJ AF: 0.107

Gnomad4 EAS AF: 0.0922

Gnomad4 SAS AF: 0.111

Gnomad4 FIN AF: 0.0520

Gnomad4 NFE AF: 0.0931

Gnomad4 OTH AF: 0.154

Alfa AF: 0.114 Hom.: 753

Bravo AF: 0.183

Asia WGS AF: 0.111 AC: 386 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.87
DANN	Benign	0.23

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2197040; hg19: chr11-13182782;