rs1431573

Variant names:

• chr11-127606864-C-T
• rs1431573

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.386 AC: 16003 AN: 41424

American (AMR) AF: 0.559 AC: 8542 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.649 AC: 2255 AN: 3472

East Asian (EAS) AF: 0.837 AC: 4320 AN: 5164

South Asian (SAS) AF: 0.569 AC: 2741 AN: 4818

European-Finnish (FIN) AF: 0.680 AC: 7188 AN: 10576

Middle Eastern (MID) AF: 0.602 AC: 177 AN: 294

European-Non Finnish (NFE) AF: 0.568 AC: 38580 AN: 67960

Other (OTH) AF: 0.540 AC: 1141 AN: 2114

Alfa AF: 0.546 Hom.: 3979

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
PhyloP100		0.43

Splicing

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

Other links and lift over

dbSNP: rs1431573; hg19: chr11-127476759;