rs11583191

chr1-186684418-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 0.135 in 151,780 control chromosomes in the GnomAD database, including 1,462 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 (1462 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.174

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.151 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: 0.135 AC: 20405 AN: 151660 Hom.: 1453 Cov.: 32

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.0329

Gnomad AMR AF: 0.143

Gnomad ASJ AF: 0.207

Gnomad EAS AF: 0.0461

Gnomad SAS AF: 0.137

Gnomad FIN AF: 0.0699

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.134

Gnomad OTH AF: 0.156

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

GnomAD4 genome AF: 0.135 AC: 20434 AN: 151780 Hom.: 1462 Cov.: 32 AF XY: 0.131 AC XY: 9707 AN XY: 74164

Gnomad4 AFR AF: 0.154

Gnomad4 AMR AF: 0.144

Gnomad4 ASJ AF: 0.207

Gnomad4 EAS AF: 0.0459

Gnomad4 SAS AF: 0.137

Gnomad4 FIN AF: 0.0699

Gnomad4 NFE AF: 0.134

Gnomad4 OTH AF: 0.159

Alfa AF: 0.139 Hom.: 235

Bravo AF: 0.143

Asia WGS AF: 0.133 AC: 463 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	1.1
Dann	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11583191; hg19: chr1-186653550;