5-159433628-T-C

Variant names:

• chr5-159433628-T-C
• rs10515802
• ENST00000635333.1:n.524+9527T>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000636261.1(ENSG00000249738):​n.367+9498T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.235 in 151,850 control chromosomes in the GnomAD database, including 5,011 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 0.24 (5011 hom., cov: 32)
• Consequence: ENSG00000249738 ENST00000636261.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.86

Genes affected

ENSG00000249738 (HGNC:58156):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.07).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.395 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
ENSG00000249738	ENST00000635333.1	n.524+9527T>C		intron_variant	Intron 6 of 7	5
ENSG00000249738	ENST00000636261.1	n.367+9498T>C		intron_variant	Intron 2 of 2	4

Frequencies

GnomAD3 genomes AF: 0.235 AC: 35632 AN: 151730 Hom.: 4991 Cov.: 32

Gnomad AFR AF: 0.399

Gnomad AMI AF: 0.180

Gnomad AMR AF: 0.152

Gnomad ASJ AF: 0.183

Gnomad EAS AF: 0.122

Gnomad SAS AF: 0.152

Gnomad FIN AF: 0.126

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.189

Gnomad OTH AF: 0.212

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

GnomAD4 genome AF: 0.235 AC: 35695 AN: 151850 Hom.: 5011 Cov.: 32 AF XY: 0.229 AC XY: 16966 AN XY: 74236

Gnomad4 AFR AF: 0.400

Gnomad4 AMR AF: 0.152

Gnomad4 ASJ AF: 0.183

Gnomad4 EAS AF: 0.122

Gnomad4 SAS AF: 0.152

Gnomad4 FIN AF: 0.126

Gnomad4 NFE AF: 0.189

Gnomad4 OTH AF: 0.211

Alfa AF: 0.191 Hom.: 3003

Bravo AF: 0.244

Asia WGS AF: 0.144 AC: 504 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.074
DANN	Benign	0.11

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10515802; hg19: chr5-158860636;