rs4313118

chr8-127559514-T-Cchr8-127559514-T-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 0.217 in 152,090 control chromosomes in the GnomAD database, including 4,188 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 0.22 (4188 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.174

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 = 0.619 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: 0.217 AC: 32943 AN: 151972 Hom.: 4179 Cov.: 32

Gnomad AFR AF: 0.202

Gnomad AMI AF: 0.372

Gnomad AMR AF: 0.187

Gnomad ASJ AF: 0.241

Gnomad EAS AF: 0.637

Gnomad SAS AF: 0.366

Gnomad FIN AF: 0.175

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.193

Gnomad OTH AF: 0.207

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

GnomAD4 genome AF: 0.217 AC: 32981 AN: 152090 Hom.: 4188 Cov.: 32 AF XY: 0.224 AC XY: 16644 AN XY: 74338

Gnomad4 AFR AF: 0.203

Gnomad4 AMR AF: 0.187

Gnomad4 ASJ AF: 0.241

Gnomad4 EAS AF: 0.637

Gnomad4 SAS AF: 0.366

Gnomad4 FIN AF: 0.175

Gnomad4 NFE AF: 0.193

Gnomad4 OTH AF: 0.209

Alfa AF: 0.199 Hom.: 5794

Bravo AF: 0.219

Asia WGS AF: 0.467 AC: 1619 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	2.3
Dann	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4313118; hg19: chr8-128571759;