rs4432842

Variant names:

• chr5-57876251-T-C
• rs4432842
• ENST00000761558.1:n.54-434T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000761558.1(ENSG00000299201):​n.54-434T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: ENSG00000299201 ENST00000761558.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.147
• Publications: 20 publications found

Genes affected

ENSG00000299201 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000299201	ENST00000761558.1	n.54-434T>C		intron_variant	Intron 1 of 3
ENSG00000299201	ENST00000761559.1	n.52+3913T>C		intron_variant	Intron 1 of 3
ENSG00000299201	ENST00000761560.1	n.53+3913T>C		intron_variant	Intron 1 of 1

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

African (AFR) AF: 0.744 AC: 30755 AN: 41346

American (AMR) AF: 0.499 AC: 7607 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.157 AC: 546 AN: 3468

East Asian (EAS) AF: 0.404 AC: 2089 AN: 5170

South Asian (SAS) AF: 0.448 AC: 2151 AN: 4800

European-Finnish (FIN) AF: 0.318 AC: 3234 AN: 10176

Middle Eastern (MID) AF: 0.277 AC: 81 AN: 292

European-Non Finnish (NFE) AF: 0.299 AC: 20268 AN: 67824

Other (OTH) AF: 0.402 AC: 843 AN: 2096

Alfa AF: 0.349 Hom.: 33243

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
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs4432842; hg19: chr5-57172078;