rs11987875

chr8-125459893-G-A

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 0.0821 in 152,142 control chromosomes in the GnomAD database, including 1,149 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 0.082 (1149 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.191

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.345 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: 0.0820 AC: 12468 AN: 152024 Hom.: 1147 Cov.: 32

Gnomad AFR AF: 0.192

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0623

Gnomad ASJ AF: 0.0199

Gnomad EAS AF: 0.358

Gnomad SAS AF: 0.0998

Gnomad FIN AF: 0.0232

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0113

Gnomad OTH AF: 0.0656

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

GnomAD4 genome AF: 0.0821 AC: 12498 AN: 152142 Hom.: 1149 Cov.: 32 AF XY: 0.0841 AC XY: 6259 AN XY: 74380

Gnomad4 AFR AF: 0.192

Gnomad4 AMR AF: 0.0624

Gnomad4 ASJ AF: 0.0199

Gnomad4 EAS AF: 0.359

Gnomad4 SAS AF: 0.0988

Gnomad4 FIN AF: 0.0232

Gnomad4 NFE AF: 0.0112

Gnomad4 OTH AF: 0.0697

Alfa AF: 0.0523 Hom.: 144

Bravo AF: 0.0919

Asia WGS AF: 0.212 AC: 735 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	6.9
Dann	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11987875; hg19: chr8-126472135;