rs1425392

Positions:

• chr4-64526494-T-C

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 0.229 in 151,920 control chromosomes in the GnomAD database, including 4,585 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 0.23 (4585 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.214

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.346 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.229 AC: 34829 AN: 151802 Hom.: 4585 Cov.: 31

Gnomad AFR AF: 0.0959

Gnomad AMI AF: 0.276

Gnomad AMR AF: 0.265

Gnomad ASJ AF: 0.347

Gnomad EAS AF: 0.322

Gnomad SAS AF: 0.361

Gnomad FIN AF: 0.266

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.273

Gnomad OTH AF: 0.258

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

GnomAD4 genome AF: 0.229 AC: 34826 AN: 151920 Hom.: 4585 Cov.: 31 AF XY: 0.229 AC XY: 17029 AN XY: 74238

Gnomad4 AFR AF: 0.0957

Gnomad4 AMR AF: 0.265

Gnomad4 ASJ AF: 0.347

Gnomad4 EAS AF: 0.322

Gnomad4 SAS AF: 0.360

Gnomad4 FIN AF: 0.266

Gnomad4 NFE AF: 0.273

Gnomad4 OTH AF: 0.260

Alfa AF: 0.278 Hom.: 5955

Bravo AF: 0.222

Asia WGS AF: 0.308 AC: 1072 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.8
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1425392; hg19: chr4-65392212;