chr8-114678422-A-G

Variant names:

• chr8-114678422-A-G
• rs7003117

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.787 AC: 32633 AN: 41488

American (AMR) AF: 0.544 AC: 8289 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.436 AC: 1510 AN: 3464

East Asian (EAS) AF: 0.897 AC: 4633 AN: 5164

South Asian (SAS) AF: 0.598 AC: 2884 AN: 4820

European-Finnish (FIN) AF: 0.399 AC: 4220 AN: 10584

Middle Eastern (MID) AF: 0.578 AC: 170 AN: 294

European-Non Finnish (NFE) AF: 0.359 AC: 24342 AN: 67892

Other (OTH) AF: 0.503 AC: 1064 AN: 2114

Alfa AF: 0.480 Hom.: 16151

Bravo AF: 0.552

Asia WGS AF: 0.725 AC: 2520 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.090
DANN	Benign	0.46
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs7003117; hg19: chr8-115690651;