rs11987056

chr8-119530407-A-G

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.203

Gnomad4 AMR AF: 0.471

Gnomad4 ASJ AF: 0.439

Gnomad4 EAS AF: 0.339

Gnomad4 SAS AF: 0.582

Gnomad4 FIN AF: 0.518

Gnomad4 NFE AF: 0.440

Gnomad4 OTH AF: 0.396

Alfa AF: 0.420 Hom.: 2212

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11987056; hg19: chr8-120542647;