4-64526494-T-C

Variant names:

• chr4-64526494-T-C
• rs1425392

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 0.229 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.0957 AC: 3970 AN: 41484

American (AMR) AF: 0.265 AC: 4034 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.347 AC: 1202 AN: 3468

East Asian (EAS) AF: 0.322 AC: 1654 AN: 5138

South Asian (SAS) AF: 0.360 AC: 1729 AN: 4808

European-Finnish (FIN) AF: 0.266 AC: 2806 AN: 10568

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.273 AC: 18526 AN: 67908

Other (OTH) AF: 0.260 AC: 550 AN: 2112

Alfa AF: 0.270 Hom.: 7452

Bravo AF: 0.222

Asia WGS AF: 0.308 AC: 1072 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.8
DANN	Benign	0.29
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs1425392; hg19: chr4-65392212;