rs11587393

chr1-27933809-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 0.131 in 99,944 control chromosomes in the GnomAD database, including 791 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 0.13 (791 hom., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.315

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.2 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: 0.131 AC: 13127 AN: 99852 Hom.: 791 Cov.: 22

Gnomad AFR AF: 0.0326

Gnomad AMI AF: 0.0775

Gnomad AMR AF: 0.121

Gnomad ASJ AF: 0.143

Gnomad EAS AF: 0.00296

Gnomad SAS AF: 0.0857

Gnomad FIN AF: 0.188

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.203

Gnomad OTH AF: 0.144

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

GnomAD4 genome AF: 0.131 AC: 13125 AN: 99944 Hom.: 791 Cov.: 22 AF XY: 0.129 AC XY: 6233 AN XY: 48336

Gnomad4 AFR AF: 0.0325

Gnomad4 AMR AF: 0.120

Gnomad4 ASJ AF: 0.143

Gnomad4 EAS AF: 0.00296

Gnomad4 SAS AF: 0.0874

Gnomad4 FIN AF: 0.188

Gnomad4 NFE AF: 0.203

Gnomad4 OTH AF: 0.143

Alfa AF: 0.122 Hom.: 1215

Bravo AF: 0.0805

Asia WGS AF: 0.0260 AC: 92 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	1.3
Dann	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11587393; hg19: chr1-28260320; COSMIC: COSV65870277;