rs4871598

Variant names:

• chr8-125447748-G-A
• rs4871598

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 0.378 in 152,132 control chromosomes in the GnomAD database, including 12,169 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 0.38 (12169 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.963

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.702 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: 0.377 AC: 57354 AN: 152014 Hom.: 12150 Cov.: 33

Gnomad AFR AF: 0.499

Gnomad AMI AF: 0.149

Gnomad AMR AF: 0.477

Gnomad ASJ AF: 0.331

Gnomad EAS AF: 0.722

Gnomad SAS AF: 0.478

Gnomad FIN AF: 0.252

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.273

Gnomad OTH AF: 0.352

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

GnomAD4 genome AF: 0.378 AC: 57442 AN: 152132 Hom.: 12169 Cov.: 33 AF XY: 0.384 AC XY: 28526 AN XY: 74360

Gnomad4 AFR AF: 0.500

Gnomad4 AMR AF: 0.478

Gnomad4 ASJ AF: 0.331

Gnomad4 EAS AF: 0.721

Gnomad4 SAS AF: 0.479

Gnomad4 FIN AF: 0.252

Gnomad4 NFE AF: 0.273

Gnomad4 OTH AF: 0.355

Alfa AF: 0.299 Hom.: 9425

Bravo AF: 0.402

Asia WGS AF: 0.553 AC: 1920 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.29
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4871598; hg19: chr8-126459990;