rs11987056

Variant names:

• chr8-119530407-A-G
• rs11987056

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.385 in 152,040 control chromosomes in the GnomAD database, including 12,435 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 0.38 (12435 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.954
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.35).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.564 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: 0.385 AC: 58490 AN: 151922 Hom.: 12435 Cov.: 32

Gnomad AFR AF: 0.204

Gnomad AMI AF: 0.535

Gnomad AMR AF: 0.471

Gnomad ASJ AF: 0.439

Gnomad EAS AF: 0.338

Gnomad SAS AF: 0.582

Gnomad FIN AF: 0.518

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.440

Gnomad OTH AF: 0.392

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

GnomAD4 genome AF: 0.385 AC: 58512 AN: 152040 Hom.: 12435 Cov.: 32 AF XY: 0.393 AC XY: 29228 AN XY: 74304

African (AFR) AF: 0.203 AC: 8439 AN: 41494

American (AMR) AF: 0.471 AC: 7196 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.439 AC: 1523 AN: 3472

East Asian (EAS) AF: 0.339 AC: 1749 AN: 5164

South Asian (SAS) AF: 0.582 AC: 2805 AN: 4822

European-Finnish (FIN) AF: 0.518 AC: 5467 AN: 10556

Middle Eastern (MID) AF: 0.364 AC: 107 AN: 294

European-Non Finnish (NFE) AF: 0.440 AC: 29906 AN: 67946

Other (OTH) AF: 0.396 AC: 834 AN: 2108

Alfa AF: 0.414 Hom.: 2239

Bravo AF: 0.367

Asia WGS AF: 0.486 AC: 1688 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.35
CADD	Benign	13
DANN	Benign	0.75
PhyloP100		0.95

Splicing

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

Other links and lift over

dbSNP: rs11987056; hg19: chr8-120542647;