5-4292503-T-C

Variant names:

• chr5-4292503-T-C
• rs1039603

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 0.444 in 152,062 control chromosomes in the GnomAD database, including 15,443 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 0.44 (15443 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.93

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.53 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: 0.444 AC: 67480 AN: 151948 Hom.: 15425 Cov.: 32

Gnomad AFR AF: 0.536

Gnomad AMI AF: 0.443

Gnomad AMR AF: 0.439

Gnomad ASJ AF: 0.445

Gnomad EAS AF: 0.312

Gnomad SAS AF: 0.452

Gnomad FIN AF: 0.391

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.406

Gnomad OTH AF: 0.471

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

GnomAD4 genome AF: 0.444 AC: 67538 AN: 152062 Hom.: 15443 Cov.: 32 AF XY: 0.442 AC XY: 32881 AN XY: 74326

Gnomad4 AFR AF: 0.536

Gnomad4 AMR AF: 0.439

Gnomad4 ASJ AF: 0.445

Gnomad4 EAS AF: 0.311

Gnomad4 SAS AF: 0.452

Gnomad4 FIN AF: 0.391

Gnomad4 NFE AF: 0.406

Gnomad4 OTH AF: 0.473

Alfa AF: 0.414 Hom.: 6217

Bravo AF: 0.452

Asia WGS AF: 0.424 AC: 1474 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	0.048
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1039603; hg19: chr5-4292616;