rs11591084

Variant names:

• chr1-79839027-T-A
• rs11591084

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 0.36 in 151,940 control chromosomes in the GnomAD database, including 12,131 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 0.36 (12131 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0810
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.46 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: 0.360 AC: 54730 AN: 151822 Hom.: 12137 Cov.: 32

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.395

Gnomad AMR AF: 0.461

Gnomad ASJ AF: 0.527

Gnomad EAS AF: 0.0547

Gnomad SAS AF: 0.369

Gnomad FIN AF: 0.567

Gnomad MID AF: 0.477

Gnomad NFE AF: 0.464

Gnomad OTH AF: 0.393

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

GnomAD4 genome AF: 0.360 AC: 54716 AN: 151940 Hom.: 12131 Cov.: 32 AF XY: 0.365 AC XY: 27118 AN XY: 74256

African (AFR) AF: 0.120 AC: 4993 AN: 41518

American (AMR) AF: 0.461 AC: 7020 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.527 AC: 1827 AN: 3468

East Asian (EAS) AF: 0.0548 AC: 283 AN: 5160

South Asian (SAS) AF: 0.368 AC: 1772 AN: 4820

European-Finnish (FIN) AF: 0.567 AC: 5992 AN: 10568

Middle Eastern (MID) AF: 0.479 AC: 137 AN: 286

European-Non Finnish (NFE) AF: 0.464 AC: 31514 AN: 67868

Other (OTH) AF: 0.389 AC: 819 AN: 2108

Alfa AF: 0.408 Hom.: 1986

Bravo AF: 0.341

Asia WGS AF: 0.209 AC: 728 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.0
DANN	Benign	0.33
PhyloP100		0.081

Splicing

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

Other links and lift over

dbSNP: rs11591084; hg19: chr1-80304712; COSMIC: COSV59960912;