rs11580589

Variant names:

• chr1-30056442-A-G
• rs11580589

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 0.192 in 152,222 control chromosomes in the GnomAD database, including 3,612 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 0.19 (3612 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.394
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.282 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: 0.192 AC: 29193 AN: 152102 Hom.: 3614 Cov.: 33

Gnomad AFR AF: 0.0607

Gnomad AMI AF: 0.282

Gnomad AMR AF: 0.169

Gnomad ASJ AF: 0.266

Gnomad EAS AF: 0.000769

Gnomad SAS AF: 0.109

Gnomad FIN AF: 0.232

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.285

Gnomad OTH AF: 0.213

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

GnomAD4 genome AF: 0.192 AC: 29188 AN: 152222 Hom.: 3612 Cov.: 33 AF XY: 0.187 AC XY: 13944 AN XY: 74410

African (AFR) AF: 0.0606 AC: 2517 AN: 41560

American (AMR) AF: 0.169 AC: 2582 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.266 AC: 924 AN: 3470

East Asian (EAS) AF: 0.000963 AC: 5 AN: 5190

South Asian (SAS) AF: 0.110 AC: 530 AN: 4828

European-Finnish (FIN) AF: 0.232 AC: 2455 AN: 10576

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.285 AC: 19407 AN: 67994

Other (OTH) AF: 0.211 AC: 446 AN: 2112

Alfa AF: 0.228 Hom.: 811

Bravo AF: 0.182

Asia WGS AF: 0.0580 AC: 202 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.56
DANN	Benign	0.54
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs11580589; hg19: chr1-30529289;