rs6431223

Variant names:

• chr2-127137911-G-A
• rs6431223

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 0.272 in 152,122 control chromosomes in the GnomAD database, including 5,860 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 0.27 (5860 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.948

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.403 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: 0.272 AC: 41354 AN: 152002 Hom.: 5859 Cov.: 34

Gnomad AFR AF: 0.222

Gnomad AMI AF: 0.341

Gnomad AMR AF: 0.331

Gnomad ASJ AF: 0.332

Gnomad EAS AF: 0.420

Gnomad SAS AF: 0.191

Gnomad FIN AF: 0.334

Gnomad MID AF: 0.296

Gnomad NFE AF: 0.269

Gnomad OTH AF: 0.296

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

GnomAD4 genome AF: 0.272 AC: 41368 AN: 152122 Hom.: 5860 Cov.: 34 AF XY: 0.278 AC XY: 20663 AN XY: 74358

Gnomad4 AFR AF: 0.222

Gnomad4 AMR AF: 0.332

Gnomad4 ASJ AF: 0.332

Gnomad4 EAS AF: 0.418

Gnomad4 SAS AF: 0.192

Gnomad4 FIN AF: 0.334

Gnomad4 NFE AF: 0.269

Gnomad4 OTH AF: 0.294

Alfa AF: 0.260 Hom.: 1164

Bravo AF: 0.275

Asia WGS AF: 0.247 AC: 858 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.45
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6431223; hg19: chr2-127895487; COSMIC: COSV65958318;