rs4078240

Variant names:

• chr8-127499318-A-G
• rs4078240

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.0286 AC: 1189 AN: 41550

American (AMR) AF: 0.119 AC: 1812 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.131 AC: 454 AN: 3472

East Asian (EAS) AF: 0.259 AC: 1340 AN: 5168

South Asian (SAS) AF: 0.189 AC: 913 AN: 4818

European-Finnish (FIN) AF: 0.134 AC: 1412 AN: 10576

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.141 AC: 9557 AN: 67986

Other (OTH) AF: 0.111 AC: 235 AN: 2116

Alfa AF: 0.115 Hom.: 250

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
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs4078240; hg19: chr8-128511563;