5-54902947-T-C

Position:

• chr5-54902947-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 0.77 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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.425

Genes affected

(HGNC:):

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/exons	MANE	Protein	UniProt
		n.54902947T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;