rs11987235

Variant names:

• chr8-116629371-G-A
• rs11987235

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 0.647 in 152,106 control chromosomes in the GnomAD database, including 34,188 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 0.65 (34188 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0390
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.781 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: 0.647 AC: 98407 AN: 151988 Hom.: 34198 Cov.: 32

Gnomad AFR AF: 0.395

Gnomad AMI AF: 0.821

Gnomad AMR AF: 0.602

Gnomad ASJ AF: 0.684

Gnomad EAS AF: 0.497

Gnomad SAS AF: 0.704

Gnomad FIN AF: 0.816

Gnomad MID AF: 0.809

Gnomad NFE AF: 0.787

Gnomad OTH AF: 0.683

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

GnomAD4 genome AF: 0.647 AC: 98420 AN: 152106 Hom.: 34188 Cov.: 32 AF XY: 0.648 AC XY: 48198 AN XY: 74374

African (AFR) AF: 0.394 AC: 16339 AN: 41464

American (AMR) AF: 0.602 AC: 9191 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.684 AC: 2374 AN: 3472

East Asian (EAS) AF: 0.498 AC: 2570 AN: 5158

South Asian (SAS) AF: 0.704 AC: 3399 AN: 4828

European-Finnish (FIN) AF: 0.816 AC: 8642 AN: 10594

Middle Eastern (MID) AF: 0.801 AC: 234 AN: 292

European-Non Finnish (NFE) AF: 0.787 AC: 53484 AN: 67996

Other (OTH) AF: 0.682 AC: 1438 AN: 2110

Alfa AF: 0.730 Hom.: 152123

Bravo AF: 0.622

Asia WGS AF: 0.584 AC: 2031 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.43
DANN	Benign	0.68
PhyloP100		-0.039

Splicing

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

Other links and lift over

dbSNP: rs11987235; hg19: chr8-117641610;