8-114678422-A-G

Variant names:

• chr8-114678422-A-G
• rs7003117

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 0.526 in 151,956 control chromosomes in the GnomAD database, including 23,996 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 0.53 (23996 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.46

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.876 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: 0.526 AC: 79886 AN: 151838 Hom.: 23947 Cov.: 32

Gnomad AFR AF: 0.786

Gnomad AMI AF: 0.277

Gnomad AMR AF: 0.544

Gnomad ASJ AF: 0.436

Gnomad EAS AF: 0.898

Gnomad SAS AF: 0.598

Gnomad FIN AF: 0.399

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.358

Gnomad OTH AF: 0.503

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

GnomAD4 genome AF: 0.526 AC: 79998 AN: 151956 Hom.: 23996 Cov.: 32 AF XY: 0.533 AC XY: 39559 AN XY: 74276

Gnomad4 AFR AF: 0.787

Gnomad4 AMR AF: 0.544

Gnomad4 ASJ AF: 0.436

Gnomad4 EAS AF: 0.897

Gnomad4 SAS AF: 0.598

Gnomad4 FIN AF: 0.399

Gnomad4 NFE AF: 0.359

Gnomad4 OTH AF: 0.503

Alfa AF: 0.421 Hom.: 7634

Bravo AF: 0.552

Asia WGS AF: 0.725 AC: 2520 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.090
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: rs7003117; hg19: chr8-115690651;