8-139321079-G-T

Variant names:

• chr8-139321079-G-T
• rs994770

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 0.581 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

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 (NFE) allele frequency at 95% confidence interval = 0.589 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: 0.581 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

Gnomad4 AFR AF: 0.586

Gnomad4 AMR AF: 0.535

Gnomad4 ASJ AF: 0.552

Gnomad4 EAS AF: 0.497

Gnomad4 SAS AF: 0.584

Gnomad4 FIN AF: 0.606

Gnomad4 NFE AF: 0.594

Gnomad4 OTH AF: 0.552

Alfa AF: 0.585 Hom.: 51944

Bravo AF: 0.573

Asia WGS AF: 0.537 AC: 1869 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs994770; hg19: chr8-140333323;