rs11586273

Variant names:

• chr1-115869329-G-A
• rs11586273

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 0.306 in 151,982 control chromosomes in the GnomAD database, including 7,321 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 0.31 (7321 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.207
• Publications: 2 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 (EAS) allele frequency at 95% confidence interval = 0.445 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.306 AC: 46445 AN: 151864 Hom.: 7311 Cov.: 32

Gnomad AFR AF: 0.218

Gnomad AMI AF: 0.354

Gnomad AMR AF: 0.383

Gnomad ASJ AF: 0.422

Gnomad EAS AF: 0.460

Gnomad SAS AF: 0.346

Gnomad FIN AF: 0.325

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.316

Gnomad OTH AF: 0.354

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

GnomAD4 genome AF: 0.306 AC: 46473 AN: 151982 Hom.: 7321 Cov.: 32 AF XY: 0.309 AC XY: 22977 AN XY: 74252

African (AFR) AF: 0.218 AC: 9053 AN: 41476

American (AMR) AF: 0.382 AC: 5836 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.422 AC: 1463 AN: 3466

East Asian (EAS) AF: 0.460 AC: 2378 AN: 5164

South Asian (SAS) AF: 0.345 AC: 1661 AN: 4812

European-Finnish (FIN) AF: 0.325 AC: 3430 AN: 10540

Middle Eastern (MID) AF: 0.459 AC: 135 AN: 294

European-Non Finnish (NFE) AF: 0.316 AC: 21440 AN: 67946

Other (OTH) AF: 0.357 AC: 755 AN: 2114

Alfa AF: 0.329 Hom.: 6305

Bravo AF: 0.309

Asia WGS AF: 0.368 AC: 1276 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.1
DANN	Benign	0.73
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs11586273; hg19: chr1-116411950;