chr8-139321079-G-T

Variant names:

• chr8-139321079-G-T
• rs994770

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 0.581 in 151,814 control chromosomes in the GnomAD database, including 25,708 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 0.58 (25708 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.41
• Publications: 1 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 (NFE) allele frequency at 95% confidence interval = 0.589 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.581 AC: 88159 AN: 151698 Hom.: 25691 Cov.: 31

Gnomad AFR AF: 0.586

Gnomad AMI AF: 0.579

Gnomad AMR AF: 0.535

Gnomad ASJ AF: 0.552

Gnomad EAS AF: 0.497

Gnomad SAS AF: 0.582

Gnomad FIN AF: 0.606

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.594

Gnomad OTH AF: 0.552

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

GnomAD4 genome AF: 0.581 AC: 88224 AN: 151814 Hom.: 25708 Cov.: 31 AF XY: 0.580 AC XY: 43033 AN XY: 74176

African (AFR) AF: 0.586 AC: 24260 AN: 41412

American (AMR) AF: 0.535 AC: 8162 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.552 AC: 1914 AN: 3466

East Asian (EAS) AF: 0.497 AC: 2534 AN: 5102

South Asian (SAS) AF: 0.584 AC: 2809 AN: 4812

European-Finnish (FIN) AF: 0.606 AC: 6390 AN: 10544

Middle Eastern (MID) AF: 0.490 AC: 144 AN: 294

European-Non Finnish (NFE) AF: 0.594 AC: 40325 AN: 67910

Other (OTH) AF: 0.552 AC: 1161 AN: 2102

Alfa AF: 0.588 Hom.: 110113

Bravo AF: 0.573

Asia WGS AF: 0.537 AC: 1869 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.3
DANN	Benign	0.47
PhyloP100		1.4

Splicing

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

Other links and lift over

dbSNP: rs994770; hg19: chr8-140333323;