rs11987875

Variant names:

• chr8-125459893-G-A
• rs11987875

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 0.0821 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
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.192 AC: 7978 AN: 41472

American (AMR) AF: 0.0624 AC: 954 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0199 AC: 69 AN: 3470

East Asian (EAS) AF: 0.359 AC: 1854 AN: 5170

South Asian (SAS) AF: 0.0988 AC: 477 AN: 4828

European-Finnish (FIN) AF: 0.0232 AC: 246 AN: 10596

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0112 AC: 764 AN: 68010

Other (OTH) AF: 0.0697 AC: 147 AN: 2110

Alfa AF: 0.0558 Hom.: 436

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
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs11987875; hg19: chr8-126472135;