chr8-119513743-G-A

Position:

• chr8-119513743-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 0.0931 in 152,086 control chromosomes in the GnomAD database, including 1,779 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 0.093 (1779 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.183

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.282 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: 0.0929 AC: 14121 AN: 151968 Hom.: 1772 Cov.: 32

Gnomad AFR AF: 0.286

Gnomad AMI AF: 0.00769

Gnomad AMR AF: 0.0448

Gnomad ASJ AF: 0.0499

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0388

Gnomad FIN AF: 0.0108

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0144

Gnomad OTH AF: 0.0720

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

GnomAD4 genome AF: 0.0931 AC: 14161 AN: 152086 Hom.: 1779 Cov.: 32 AF XY: 0.0910 AC XY: 6769 AN XY: 74356

Gnomad4 AFR AF: 0.286

Gnomad4 AMR AF: 0.0447

Gnomad4 ASJ AF: 0.0499

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.0386

Gnomad4 FIN AF: 0.0108

Gnomad4 NFE AF: 0.0144

Gnomad4 OTH AF: 0.0712

Alfa AF: 0.0491 Hom.: 291

Bravo AF: 0.104

Asia WGS AF: 0.0300 AC: 104 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	4.8
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16892701; hg19: chr8-120525983;