rs11587500

chr1-24190390-G-Achr1-24190390-G-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.332

Gnomad4 AMR AF: 0.334

Gnomad4 ASJ AF: 0.501

Gnomad4 EAS AF: 0.140

Gnomad4 SAS AF: 0.571

Gnomad4 FIN AF: 0.453

Gnomad4 NFE AF: 0.490

Gnomad4 OTH AF: 0.430

Alfa AF: 0.476 Hom.: 22884

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11587500; hg19: chr1-24516880;