8-139246954-C-T

Position:

• chr8-139246954-C-T

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 0.368 in 151,540 control chromosomes in the GnomAD database, including 11,209 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 0.37 (11209 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.459

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.467 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.368 AC: 55794 AN: 151422 Hom.: 11197 Cov.: 32

Gnomad AFR AF: 0.230

Gnomad AMI AF: 0.313

Gnomad AMR AF: 0.476

Gnomad ASJ AF: 0.407

Gnomad EAS AF: 0.233

Gnomad SAS AF: 0.335

Gnomad FIN AF: 0.464

Gnomad MID AF: 0.283

Gnomad NFE AF: 0.426

Gnomad OTH AF: 0.355

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

GnomAD4 genome AF: 0.368 AC: 55816 AN: 151540 Hom.: 11209 Cov.: 32 AF XY: 0.372 AC XY: 27546 AN XY: 74070

Gnomad4 AFR AF: 0.229

Gnomad4 AMR AF: 0.476

Gnomad4 ASJ AF: 0.407

Gnomad4 EAS AF: 0.232

Gnomad4 SAS AF: 0.336

Gnomad4 FIN AF: 0.464

Gnomad4 NFE AF: 0.426

Gnomad4 OTH AF: 0.351

Alfa AF: 0.404 Hom.: 4289

Bravo AF: 0.360

Asia WGS AF: 0.286 AC: 1000 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.9
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: rs7006032; hg19: chr8-140259197;