5-54902947-T-C

Variant names:

• chr5-54902947-T-C
• rs4242051

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 0.77 in 152,106 control chromosomes in the GnomAD database, including 45,210 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 0.77 (45210 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.425

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.8 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: 0.770 AC: 116971 AN: 151988 Hom.: 45172 Cov.: 32

Gnomad AFR AF: 0.808

Gnomad AMI AF: 0.633

Gnomad AMR AF: 0.796

Gnomad ASJ AF: 0.758

Gnomad EAS AF: 0.656

Gnomad SAS AF: 0.747

Gnomad FIN AF: 0.763

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.755

Gnomad OTH AF: 0.764

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

GnomAD4 genome AF: 0.770 AC: 117060 AN: 152106 Hom.: 45210 Cov.: 32 AF XY: 0.769 AC XY: 57130 AN XY: 74332

Gnomad4 AFR AF: 0.808

Gnomad4 AMR AF: 0.797

Gnomad4 ASJ AF: 0.758

Gnomad4 EAS AF: 0.655

Gnomad4 SAS AF: 0.746

Gnomad4 FIN AF: 0.763

Gnomad4 NFE AF: 0.755

Gnomad4 OTH AF: 0.763

Alfa AF: 0.744 Hom.: 7878

Bravo AF: 0.774

Asia WGS AF: 0.723 AC: 2513 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.2
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4242051; hg19: chr5-54198775;