rs1078425

Variant names:

• chr5-123337366-G-T
• rs1078425

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 0.168 in 152,012 control chromosomes in the GnomAD database, including 2,631 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 0.17 (2631 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.133

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.222 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: 0.168 AC: 25583 AN: 151894 Hom.: 2634 Cov.: 32

Gnomad AFR AF: 0.0591

Gnomad AMI AF: 0.212

Gnomad AMR AF: 0.157

Gnomad ASJ AF: 0.181

Gnomad EAS AF: 0.151

Gnomad SAS AF: 0.183

Gnomad FIN AF: 0.240

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.225

Gnomad OTH AF: 0.188

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

GnomAD4 genome AF: 0.168 AC: 25578 AN: 152012 Hom.: 2631 Cov.: 32 AF XY: 0.169 AC XY: 12556 AN XY: 74288

Gnomad4 AFR AF: 0.0589

Gnomad4 AMR AF: 0.157

Gnomad4 ASJ AF: 0.181

Gnomad4 EAS AF: 0.152

Gnomad4 SAS AF: 0.183

Gnomad4 FIN AF: 0.240

Gnomad4 NFE AF: 0.225

Gnomad4 OTH AF: 0.187

Alfa AF: 0.184 Hom.: 1178

Bravo AF: 0.160

Asia WGS AF: 0.119 AC: 414 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.7
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1078425; hg19: chr5-122673060;