rs4357259

chr8-110823464-C-Achr8-110823464-C-G

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 0.773 in 151,752 control chromosomes in the GnomAD database, including 46,084 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 0.77 (46084 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.04

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 (NFE) allele frequency at 95% confidence interval = 0.835 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.773 AC: 117234 AN: 151636 Hom.: 46041 Cov.: 30

Gnomad AFR AF: 0.729

Gnomad AMI AF: 0.944

Gnomad AMR AF: 0.680

Gnomad ASJ AF: 0.816

Gnomad EAS AF: 0.417

Gnomad SAS AF: 0.629

Gnomad FIN AF: 0.852

Gnomad MID AF: 0.812

Gnomad NFE AF: 0.841

Gnomad OTH AF: 0.783

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

GnomAD4 genome AF: 0.773 AC: 117327 AN: 151752 Hom.: 46084 Cov.: 30 AF XY: 0.766 AC XY: 56814 AN XY: 74166

Gnomad4 AFR AF: 0.729

Gnomad4 AMR AF: 0.680

Gnomad4 ASJ AF: 0.816

Gnomad4 EAS AF: 0.416

Gnomad4 SAS AF: 0.631

Gnomad4 FIN AF: 0.852

Gnomad4 NFE AF: 0.841

Gnomad4 OTH AF: 0.779

Alfa AF: 0.762 Hom.: 2383

Bravo AF: 0.761

Asia WGS AF: 0.529 AC: 1833 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.034
Dann	Benign	0.21

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4357259; hg19: chr8-111835693;