rs604127

Positions:

• chr2-31298423-G-A

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;