rs11583191

Variant names:

• chr1-186684418-G-A
• rs11583191

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 0.135 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
• Publications: 7 publications found

ACMG classification

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.154 AC: 6369 AN: 41330

American (AMR) AF: 0.144 AC: 2186 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.207 AC: 717 AN: 3470

East Asian (EAS) AF: 0.0459 AC: 237 AN: 5168

South Asian (SAS) AF: 0.137 AC: 660 AN: 4808

European-Finnish (FIN) AF: 0.0699 AC: 738 AN: 10552

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.134 AC: 9105 AN: 67920

Other (OTH) AF: 0.159 AC: 334 AN: 2104

Alfa AF: 0.138 Hom.: 242

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
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs11583191; hg19: chr1-186653550;