rs4432842

Positions:

• chr5-57876251-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 0.448 in 151,328 control chromosomes in the GnomAD database, including 18,270 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 0.45 (18270 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.147

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.737 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.57876251T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.448 AC: 67698 AN: 151228 Hom.: 18220 Cov.: 31

Gnomad AFR AF: 0.743

Gnomad AMI AF: 0.259

Gnomad AMR AF: 0.498

Gnomad ASJ AF: 0.157

Gnomad EAS AF: 0.404

Gnomad SAS AF: 0.448

Gnomad FIN AF: 0.318

Gnomad MID AF: 0.280

Gnomad NFE AF: 0.299

Gnomad OTH AF: 0.400

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

GnomAD4 genome AF: 0.448 AC: 67810 AN: 151328 Hom.: 18270 Cov.: 31 AF XY: 0.448 AC XY: 33093 AN XY: 73910

Gnomad4 AFR AF: 0.744

Gnomad4 AMR AF: 0.499

Gnomad4 ASJ AF: 0.157

Gnomad4 EAS AF: 0.404

Gnomad4 SAS AF: 0.448

Gnomad4 FIN AF: 0.318

Gnomad4 NFE AF: 0.299

Gnomad4 OTH AF: 0.402

Alfa AF: 0.330 Hom.: 10516

Bravo AF: 0.478

Asia WGS AF: 0.448 AC: 1554 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.6
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4432842; hg19: chr5-57172078;