rs1833754

Variant names:

• chr5-159391919-T-C
• rs1833754
• ENST00000635333.1:n.283-614T>C

Variant summary

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

The ENST00000635333.1(ENSG00000249738):​n.283-614T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.116 in 152,204 control chromosomes in the GnomAD database, including 1,495 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 0.12 (1495 hom., cov: 33)
• Consequence: ENSG00000249738 ENST00000635333.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.66

Genes affected

ENSG00000249738 (HGNC:58156):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.207 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.283-614T>C		intron_variant	Intron 3 of 7	5
ENSG00000249738	ENST00000641150.1	n.533-24605T>C		intron_variant	Intron 4 of 4
ENSG00000249738	ENST00000648969.1	n.54-24605T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.116 AC: 17602 AN: 152086 Hom.: 1485 Cov.: 33

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.0881

Gnomad AMR AF: 0.175

Gnomad ASJ AF: 0.0815

Gnomad EAS AF: 0.193

Gnomad SAS AF: 0.143

Gnomad FIN AF: 0.0512

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0489

Gnomad OTH AF: 0.120

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

GnomAD4 genome AF: 0.116 AC: 17648 AN: 152204 Hom.: 1495 Cov.: 33 AF XY: 0.117 AC XY: 8686 AN XY: 74428

Gnomad4 AFR AF: 0.211

Gnomad4 AMR AF: 0.176

Gnomad4 ASJ AF: 0.0815

Gnomad4 EAS AF: 0.193

Gnomad4 SAS AF: 0.142

Gnomad4 FIN AF: 0.0512

Gnomad4 NFE AF: 0.0489

Gnomad4 OTH AF: 0.123

Alfa AF: 0.0741 Hom.: 404

Bravo AF: 0.134

Asia WGS AF: 0.168 AC: 582 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.7
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1833754; hg19: chr5-158818927;