rs2444769

Positions:

• chr2-157637588-C-A
• chr2-157637588-C-G
• chr2-157637588-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 0.669 in 151,808 control chromosomes in the GnomAD database, including 37,512 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 0.67 (37512 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.668

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.822 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: 0.670 AC: 101566 AN: 151688 Hom.: 37497 Cov.: 30

Gnomad AFR AF: 0.331

Gnomad AMI AF: 0.944

Gnomad AMR AF: 0.765

Gnomad ASJ AF: 0.715

Gnomad EAS AF: 0.844

Gnomad SAS AF: 0.807

Gnomad FIN AF: 0.860

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.795

Gnomad OTH AF: 0.666

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

GnomAD4 genome AF: 0.669 AC: 101598 AN: 151808 Hom.: 37512 Cov.: 30 AF XY: 0.679 AC XY: 50394 AN XY: 74192

Gnomad4 AFR AF: 0.331

Gnomad4 AMR AF: 0.765

Gnomad4 ASJ AF: 0.715

Gnomad4 EAS AF: 0.843

Gnomad4 SAS AF: 0.808

Gnomad4 FIN AF: 0.860

Gnomad4 NFE AF: 0.795

Gnomad4 OTH AF: 0.669

Alfa AF: 0.775 Hom.: 22402

Bravo AF: 0.644

Asia WGS AF: 0.798 AC: 2762 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.5
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2444769; hg19: chr2-158494100;