rs4298458

Variant names:

• chr8-31627354-C-G
• rs4298458

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 0.536 in 151,890 control chromosomes in the GnomAD database, including 22,001 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 (22001 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.279
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.58 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: 0.536 AC: 81390 AN: 151772 Hom.: 21988 Cov.: 30

Gnomad AFR AF: 0.586

Gnomad AMI AF: 0.607

Gnomad AMR AF: 0.581

Gnomad ASJ AF: 0.442

Gnomad EAS AF: 0.420

Gnomad SAS AF: 0.530

Gnomad FIN AF: 0.465

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.521

Gnomad OTH AF: 0.506

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

GnomAD4 genome AF: 0.536 AC: 81439 AN: 151890 Hom.: 22001 Cov.: 30 AF XY: 0.533 AC XY: 39594 AN XY: 74242

African (AFR) AF: 0.586 AC: 24275 AN: 41432

American (AMR) AF: 0.581 AC: 8872 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.442 AC: 1533 AN: 3470

East Asian (EAS) AF: 0.420 AC: 2157 AN: 5140

South Asian (SAS) AF: 0.529 AC: 2545 AN: 4810

European-Finnish (FIN) AF: 0.465 AC: 4892 AN: 10516

Middle Eastern (MID) AF: 0.439 AC: 129 AN: 294

European-Non Finnish (NFE) AF: 0.521 AC: 35423 AN: 67936

Other (OTH) AF: 0.504 AC: 1061 AN: 2106

Alfa AF: 0.534 Hom.: 2712

Bravo AF: 0.547

Asia WGS AF: 0.506 AC: 1761 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.8
DANN	Benign	0.47
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs4298458; hg19: chr8-31484870;