rs1078425

Positions:

• chr5-123337366-G-T

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;