rs1427588

Variant names:

• chr2-136734756-C-T
• rs1427588

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 0.62 in 151,478 control chromosomes in the GnomAD database, including 29,449 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 0.62 (29449 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0190

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.658 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: 0.620 AC: 93904 AN: 151360 Hom.: 29435 Cov.: 29

Gnomad AFR AF: 0.620

Gnomad AMI AF: 0.699

Gnomad AMR AF: 0.622

Gnomad ASJ AF: 0.752

Gnomad EAS AF: 0.426

Gnomad SAS AF: 0.677

Gnomad FIN AF: 0.561

Gnomad MID AF: 0.713

Gnomad NFE AF: 0.631

Gnomad OTH AF: 0.649

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

GnomAD4 genome AF: 0.620 AC: 93951 AN: 151478 Hom.: 29449 Cov.: 29 AF XY: 0.619 AC XY: 45831 AN XY: 73998

Gnomad4 AFR AF: 0.620

Gnomad4 AMR AF: 0.622

Gnomad4 ASJ AF: 0.752

Gnomad4 EAS AF: 0.425

Gnomad4 SAS AF: 0.677

Gnomad4 FIN AF: 0.561

Gnomad4 NFE AF: 0.631

Gnomad4 OTH AF: 0.652

Alfa AF: 0.643 Hom.: 15028

Bravo AF: 0.622

Asia WGS AF: 0.526 AC: 1831 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.8
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1427588; hg19: chr2-137492326;