chr8-131406862-C-T

Variant names:

• chr8-131406862-C-T
• rs1430324

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 0.545 in 151,708 control chromosomes in the GnomAD database, including 23,916 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 0.54 (23916 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.23
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.07).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.75 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: 0.545 AC: 82552 AN: 151590 Hom.: 23872 Cov.: 31

Gnomad AFR AF: 0.757

Gnomad AMI AF: 0.493

Gnomad AMR AF: 0.469

Gnomad ASJ AF: 0.535

Gnomad EAS AF: 0.543

Gnomad SAS AF: 0.397

Gnomad FIN AF: 0.430

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.463

Gnomad OTH AF: 0.533

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

GnomAD4 genome AF: 0.545 AC: 82644 AN: 151708 Hom.: 23916 Cov.: 31 AF XY: 0.539 AC XY: 39926 AN XY: 74136

African (AFR) AF: 0.757 AC: 31356 AN: 41406

American (AMR) AF: 0.469 AC: 7123 AN: 15200

Ashkenazi Jewish (ASJ) AF: 0.535 AC: 1854 AN: 3468

East Asian (EAS) AF: 0.542 AC: 2785 AN: 5138

South Asian (SAS) AF: 0.397 AC: 1908 AN: 4812

European-Finnish (FIN) AF: 0.430 AC: 4535 AN: 10542

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.463 AC: 31380 AN: 67832

Other (OTH) AF: 0.533 AC: 1123 AN: 2106

Alfa AF: 0.416 Hom.: 1866

Bravo AF: 0.562

Asia WGS AF: 0.466 AC: 1620 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.13
DANN	Benign	0.15
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs1430324; hg19: chr8-132419109;