rs4078240

Variant names:

• chr8-127499318-A-G
• rs4078240

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 0.112 in 152,170 control chromosomes in the GnomAD database, including 1,248 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 0.11 (1248 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.196

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.248 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: 0.112 AC: 17083 AN: 152052 Hom.: 1249 Cov.: 32

Gnomad AFR AF: 0.0287

Gnomad AMI AF: 0.150

Gnomad AMR AF: 0.118

Gnomad ASJ AF: 0.131

Gnomad EAS AF: 0.258

Gnomad SAS AF: 0.190

Gnomad FIN AF: 0.134

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.141

Gnomad OTH AF: 0.114

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

GnomAD4 genome AF: 0.112 AC: 17081 AN: 152170 Hom.: 1248 Cov.: 32 AF XY: 0.113 AC XY: 8415 AN XY: 74396

Gnomad4 AFR AF: 0.0286

Gnomad4 AMR AF: 0.119

Gnomad4 ASJ AF: 0.131

Gnomad4 EAS AF: 0.259

Gnomad4 SAS AF: 0.189

Gnomad4 FIN AF: 0.134

Gnomad4 NFE AF: 0.141

Gnomad4 OTH AF: 0.111

Alfa AF: 0.125 Hom.: 239

Bravo AF: 0.105

Asia WGS AF: 0.174 AC: 607 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.3
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4078240; hg19: chr8-128511563;