chr8-119496864-A-G

Position:

• chr8-119496864-A-G

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 0.366 in 152,042 control chromosomes in the GnomAD database, including 11,218 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 0.37 (11218 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.282

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.565 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.366 AC: 55652 AN: 151926 Hom.: 11219 Cov.: 32

Gnomad AFR AF: 0.197

Gnomad AMI AF: 0.569

Gnomad AMR AF: 0.427

Gnomad ASJ AF: 0.415

Gnomad EAS AF: 0.298

Gnomad SAS AF: 0.584

Gnomad FIN AF: 0.473

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.424

Gnomad OTH AF: 0.372

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

GnomAD4 genome AF: 0.366 AC: 55662 AN: 152042 Hom.: 11218 Cov.: 32 AF XY: 0.372 AC XY: 27640 AN XY: 74304

Gnomad4 AFR AF: 0.196

Gnomad4 AMR AF: 0.427

Gnomad4 ASJ AF: 0.415

Gnomad4 EAS AF: 0.298

Gnomad4 SAS AF: 0.583

Gnomad4 FIN AF: 0.473

Gnomad4 NFE AF: 0.424

Gnomad4 OTH AF: 0.377

Alfa AF: 0.409 Hom.: 6998

Bravo AF: 0.349

Asia WGS AF: 0.478 AC: 1660 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.9
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10505364; hg19: chr8-120509104;