rs1431573

Variant names:

• chr11-127606864-C-T
• rs1431573

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 0.537 in 152,000 control chromosomes in the GnomAD database, including 22,898 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 0.54 (22898 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.427

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.816 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: 0.537 AC: 81565 AN: 151882 Hom.: 22890 Cov.: 32

Gnomad AFR AF: 0.386

Gnomad AMI AF: 0.732

Gnomad AMR AF: 0.559

Gnomad ASJ AF: 0.649

Gnomad EAS AF: 0.837

Gnomad SAS AF: 0.569

Gnomad FIN AF: 0.680

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.568

Gnomad OTH AF: 0.541

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

GnomAD4 genome AF: 0.537 AC: 81612 AN: 152000 Hom.: 22898 Cov.: 32 AF XY: 0.548 AC XY: 40733 AN XY: 74322

Gnomad4 AFR AF: 0.386

Gnomad4 AMR AF: 0.559

Gnomad4 ASJ AF: 0.649

Gnomad4 EAS AF: 0.837

Gnomad4 SAS AF: 0.569

Gnomad4 FIN AF: 0.680

Gnomad4 NFE AF: 0.568

Gnomad4 OTH AF: 0.540

Alfa AF: 0.550 Hom.: 3904

Bravo AF: 0.526

Asia WGS AF: 0.624 AC: 2169 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
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: rs1431573; hg19: chr11-127476759;