rs1588023

Variant names:

• chr8-139011926-G-A
• rs1588023

Your query was ambiguous. Multiple possible variants found:

• chr8-139011926-G-A
• chr8-139011926-G-C

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 0.407 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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.514 AC: 21296 AN: 41400

American (AMR) AF: 0.433 AC: 6611 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.310 AC: 1075 AN: 3468

East Asian (EAS) AF: 0.719 AC: 3721 AN: 5174

South Asian (SAS) AF: 0.515 AC: 2480 AN: 4812

European-Finnish (FIN) AF: 0.337 AC: 3543 AN: 10516

Middle Eastern (MID) AF: 0.306 AC: 90 AN: 294

European-Non Finnish (NFE) AF: 0.323 AC: 21958 AN: 67924

Other (OTH) AF: 0.373 AC: 788 AN: 2114

Alfa AF: 0.356 Hom.: 6396

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
PhyloP100		-0.72

Splicing

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

Other links and lift over

dbSNP: rs1588023; hg19: chr8-140024169;