chr8-139011926-G-A

Variant names:

• chr8-139011926-G-A
• rs1588023

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 0.407 in 151,866 control chromosomes in the GnomAD database, including 13,442 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 0.41 (13442 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.716

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.7 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: 0.407 AC: 61691 AN: 151746 Hom.: 13397 Cov.: 32

Gnomad AFR AF: 0.514

Gnomad AMI AF: 0.256

Gnomad AMR AF: 0.433

Gnomad ASJ AF: 0.310

Gnomad EAS AF: 0.718

Gnomad SAS AF: 0.515

Gnomad FIN AF: 0.337

Gnomad MID AF: 0.303

Gnomad NFE AF: 0.323

Gnomad OTH AF: 0.370

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

GnomAD4 genome AF: 0.407 AC: 61795 AN: 151866 Hom.: 13442 Cov.: 32 AF XY: 0.410 AC XY: 30400 AN XY: 74202

Gnomad4 AFR AF: 0.514

Gnomad4 AMR AF: 0.433

Gnomad4 ASJ AF: 0.310

Gnomad4 EAS AF: 0.719

Gnomad4 SAS AF: 0.515

Gnomad4 FIN AF: 0.337

Gnomad4 NFE AF: 0.323

Gnomad4 OTH AF: 0.373

Alfa AF: 0.357 Hom.: 5852

Bravo AF: 0.423

Asia WGS AF: 0.642 AC: 2231 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.96
DANN	Benign	0.22

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1588023; hg19: chr8-140024169;