8-117178154-A-G

Position:

• chr8-117178154-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 0.46 in 151,790 control chromosomes in the GnomAD database, including 17,850 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 0.46 (17850 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.21

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.799 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.117178154A>G		intergenic_region
LOC105375716	XR_007061067.1	n.560-4666T>C		intron_variant
LOC105375716	XR_007061068.1	n.947-4666T>C		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.460 AC: 69738 AN: 151674 Hom.: 17837 Cov.: 32

Gnomad AFR AF: 0.238

Gnomad AMI AF: 0.526

Gnomad AMR AF: 0.553

Gnomad ASJ AF: 0.504

Gnomad EAS AF: 0.820

Gnomad SAS AF: 0.605

Gnomad FIN AF: 0.645

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.504

Gnomad OTH AF: 0.466

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

GnomAD4 genome AF: 0.460 AC: 69772 AN: 151790 Hom.: 17850 Cov.: 32 AF XY: 0.473 AC XY: 35069 AN XY: 74176

Gnomad4 AFR AF: 0.237

Gnomad4 AMR AF: 0.554

Gnomad4 ASJ AF: 0.504

Gnomad4 EAS AF: 0.820

Gnomad4 SAS AF: 0.604

Gnomad4 FIN AF: 0.645

Gnomad4 NFE AF: 0.504

Gnomad4 OTH AF: 0.469

Alfa AF: 0.499 Hom.: 25024

Bravo AF: 0.447

Asia WGS AF: 0.625 AC: 2170 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	8.0
DANN	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2466291; hg19: chr8-118190393; COSMIC: COSV69972064;