5-5604439-T-C

Variant names:

• chr5-5604439-T-C
• rs1438675

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 0.253 in 152,130 control chromosomes in the GnomAD database, including 5,865 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 0.25 (5865 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.245

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.533 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: 0.253 AC: 38481 AN: 152012 Hom.: 5869 Cov.: 33

Gnomad AFR AF: 0.0895

Gnomad AMI AF: 0.184

Gnomad AMR AF: 0.343

Gnomad ASJ AF: 0.243

Gnomad EAS AF: 0.550

Gnomad SAS AF: 0.411

Gnomad FIN AF: 0.293

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.294

Gnomad OTH AF: 0.253

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

GnomAD4 genome AF: 0.253 AC: 38493 AN: 152130 Hom.: 5865 Cov.: 33 AF XY: 0.260 AC XY: 19366 AN XY: 74370

Gnomad4 AFR AF: 0.0894

Gnomad4 AMR AF: 0.343

Gnomad4 ASJ AF: 0.243

Gnomad4 EAS AF: 0.550

Gnomad4 SAS AF: 0.410

Gnomad4 FIN AF: 0.293

Gnomad4 NFE AF: 0.294

Gnomad4 OTH AF: 0.257

Alfa AF: 0.294 Hom.: 4672

Bravo AF: 0.249

Asia WGS AF: 0.443 AC: 1541 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.4
DANN	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1438675; hg19: chr5-5604552;