rs604127

Variant names:

• chr2-31298423-G-A
• rs604127

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 0.859 in 152,248 control chromosomes in the GnomAD database, including 56,365 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 0.86 (56365 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0270

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.957 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: 0.859 AC: 130726 AN: 152130 Hom.: 56309 Cov.: 32

Gnomad AFR AF: 0.884

Gnomad AMI AF: 0.792

Gnomad AMR AF: 0.865

Gnomad ASJ AF: 0.780

Gnomad EAS AF: 0.980

Gnomad SAS AF: 0.854

Gnomad FIN AF: 0.873

Gnomad MID AF: 0.825

Gnomad NFE AF: 0.837

Gnomad OTH AF: 0.858

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

GnomAD4 genome AF: 0.859 AC: 130840 AN: 152248 Hom.: 56365 Cov.: 32 AF XY: 0.861 AC XY: 64102 AN XY: 74458

Gnomad4 AFR AF: 0.884

Gnomad4 AMR AF: 0.865

Gnomad4 ASJ AF: 0.780

Gnomad4 EAS AF: 0.980

Gnomad4 SAS AF: 0.855

Gnomad4 FIN AF: 0.873

Gnomad4 NFE AF: 0.837

Gnomad4 OTH AF: 0.860

Alfa AF: 0.839 Hom.: 78053

Bravo AF: 0.861

Asia WGS AF: 0.918 AC: 3192 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.46
DANN	Benign	0.11

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs604127; hg19: chr2-31521289;