rs11587393

Variant names:

• chr1-27933809-G-A
• rs11587393

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 0.131 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
• Publications: 12 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.0325 AC: 912 AN: 28060

American (AMR) AF: 0.120 AC: 1239 AN: 10286

Ashkenazi Jewish (ASJ) AF: 0.143 AC: 279 AN: 1950

East Asian (EAS) AF: 0.00296 AC: 13 AN: 4390

South Asian (SAS) AF: 0.0874 AC: 213 AN: 2436

European-Finnish (FIN) AF: 0.188 AC: 1208 AN: 6426

Middle Eastern (MID) AF: 0.133 AC: 20 AN: 150

European-Non Finnish (NFE) AF: 0.203 AC: 8996 AN: 44268

Other (OTH) AF: 0.143 AC: 201 AN: 1410

Alfa AF: 0.122 Hom.: 1765

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
PhyloP100		0.32

Splicing

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

Other links and lift over

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