5-174791389-C-T

Variant names:

• chr5-174791389-C-T
• rs10476123
• ENST00000502684.1:n.50+40036C>T

Variant summary

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

The ENST00000502684.1(ENSG00000251670):​n.50+40036C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.51 (12759 hom., cov: 20)
• Consequence: ENSG00000251670 ENST00000502684.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.314
• Publications: 1 publications found

Genes affected

ENSG00000251670 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 = 0.576 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
ENSG00000251670	ENST00000502684.1	n.50+40036C>T		intron_variant	Intron 1 of 3	5
ENSG00000251670	ENST00000510150.2	n.117-28464C>T		intron_variant	Intron 1 of 3	3
ENSG00000251670	ENST00000798403.1	n.179-34733C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.513 AC: 60513 AN: 117950 Hom.: 12746 Cov.: 20

Gnomad AFR AF: 0.583

Gnomad AMI AF: 0.436

Gnomad AMR AF: 0.495

Gnomad ASJ AF: 0.504

Gnomad EAS AF: 0.399

Gnomad SAS AF: 0.373

Gnomad FIN AF: 0.571

Gnomad MID AF: 0.439

Gnomad NFE AF: 0.483

Gnomad OTH AF: 0.524

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

GnomAD4 genome AF: 0.513 AC: 60561 AN: 118024 Hom.: 12759 Cov.: 20 AF XY: 0.514 AC XY: 28974 AN XY: 56372

African (AFR) AF: 0.583 AC: 19684 AN: 33774

American (AMR) AF: 0.495 AC: 5050 AN: 10192

Ashkenazi Jewish (ASJ) AF: 0.504 AC: 1427 AN: 2830

East Asian (EAS) AF: 0.399 AC: 1462 AN: 3666

South Asian (SAS) AF: 0.373 AC: 1153 AN: 3092

European-Finnish (FIN) AF: 0.571 AC: 3966 AN: 6946

Middle Eastern (MID) AF: 0.448 AC: 94 AN: 210

European-Non Finnish (NFE) AF: 0.483 AC: 26566 AN: 54988

Other (OTH) AF: 0.525 AC: 851 AN: 1620

Alfa AF: 0.381 Hom.: 6192

Bravo AF: 0.416

Asia WGS AF: 0.310 AC: 1068 AN: 3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.9
DANN	Benign	0.53
PhyloP100		-0.31

Splicing

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

Other links and lift over

dbSNP: rs10476123; hg19: chr5-174218392;