rs2170436

Positions:

• chr11-13211191-G-A
• chr11-13211191-G-C
• chr11-13211191-G-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 0.606 in 152,004 control chromosomes in the GnomAD database, including 30,106 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 0.61 (30106 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.02

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.802 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: 0.607 AC: 92169 AN: 151886 Hom.: 30107 Cov.: 32

Gnomad AFR AF: 0.358

Gnomad AMI AF: 0.627

Gnomad AMR AF: 0.610

Gnomad ASJ AF: 0.634

Gnomad EAS AF: 0.822

Gnomad SAS AF: 0.741

Gnomad FIN AF: 0.681

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.719

Gnomad OTH AF: 0.605

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

GnomAD4 genome AF: 0.606 AC: 92183 AN: 152004 Hom.: 30106 Cov.: 32 AF XY: 0.609 AC XY: 45244 AN XY: 74292

Gnomad4 AFR AF: 0.357

Gnomad4 AMR AF: 0.610

Gnomad4 ASJ AF: 0.634

Gnomad4 EAS AF: 0.822

Gnomad4 SAS AF: 0.740

Gnomad4 FIN AF: 0.681

Gnomad4 NFE AF: 0.719

Gnomad4 OTH AF: 0.610

Alfa AF: 0.692 Hom.: 49578

Bravo AF: 0.586

Asia WGS AF: 0.745 AC: 2580 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	9.3
DANN	Benign	0.14

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2170436; hg19: chr11-13232738;