chr2-169780132-C-T

Variant names:

• chr2-169780132-C-T
• rs11894266

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 0.455 in 152,084 control chromosomes in the GnomAD database, including 16,629 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 0.45 (16629 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.651

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 (NFE) allele frequency at 95% confidence interval = 0.535 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: 0.455 AC: 69162 AN: 151966 Hom.: 16636 Cov.: 32

Gnomad AFR AF: 0.288

Gnomad AMI AF: 0.607

Gnomad AMR AF: 0.462

Gnomad ASJ AF: 0.563

Gnomad EAS AF: 0.443

Gnomad SAS AF: 0.467

Gnomad FIN AF: 0.501

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.539

Gnomad OTH AF: 0.485

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

GnomAD4 genome AF: 0.455 AC: 69174 AN: 152084 Hom.: 16629 Cov.: 32 AF XY: 0.454 AC XY: 33786 AN XY: 74342

Gnomad4 AFR AF: 0.288

Gnomad4 AMR AF: 0.462

Gnomad4 ASJ AF: 0.563

Gnomad4 EAS AF: 0.443

Gnomad4 SAS AF: 0.469

Gnomad4 FIN AF: 0.501

Gnomad4 NFE AF: 0.539

Gnomad4 OTH AF: 0.482

Alfa AF: 0.516 Hom.: 9458

Bravo AF: 0.443

Asia WGS AF: 0.405 AC: 1410 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	0.73
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11894266; hg19: chr2-170636642;