chr8-127559514-T-C

Variant names:

• chr8-127559514-T-C
• rs4313118

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;