rs11587500

Variant names:

• chr1-24190390-G-A
• rs11587500

Your query was ambiguous. Multiple possible variants found:

• chr1-24190390-G-A
• chr1-24190390-G-T

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 0.419 in 152,068 control chromosomes in the GnomAD database, including 14,231 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 0.42 (14231 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0100
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.553 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: 0.419 AC: 63718 AN: 151950 Hom.: 14228 Cov.: 32

Gnomad AFR AF: 0.332

Gnomad AMI AF: 0.565

Gnomad AMR AF: 0.334

Gnomad ASJ AF: 0.501

Gnomad EAS AF: 0.141

Gnomad SAS AF: 0.570

Gnomad FIN AF: 0.453

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.490

Gnomad OTH AF: 0.435

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

GnomAD4 genome AF: 0.419 AC: 63730 AN: 152068 Hom.: 14231 Cov.: 32 AF XY: 0.418 AC XY: 31097 AN XY: 74332

African (AFR) AF: 0.332 AC: 13761 AN: 41458

American (AMR) AF: 0.334 AC: 5102 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.501 AC: 1736 AN: 3468

East Asian (EAS) AF: 0.140 AC: 727 AN: 5178

South Asian (SAS) AF: 0.571 AC: 2753 AN: 4822

European-Finnish (FIN) AF: 0.453 AC: 4784 AN: 10556

Middle Eastern (MID) AF: 0.483 AC: 142 AN: 294

European-Non Finnish (NFE) AF: 0.490 AC: 33307 AN: 67996

Other (OTH) AF: 0.430 AC: 904 AN: 2104

Alfa AF: 0.464 Hom.: 51580

Bravo AF: 0.402

Asia WGS AF: 0.301 AC: 1047 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.0
DANN	Benign	0.74
PhyloP100		0.010

Splicing

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

Other links and lift over

dbSNP: rs11587500; hg19: chr1-24516880;