5-4292503-T-C

Position:

• chr5-4292503-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 0.444 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;