ENST00000454967.1:c.70-4847A>T

Variant names:

• chr1-84383433-A-T
• rs315511
• ENST00000454967.1:c.70-4847A>T

Variant summary

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

The ENST00000454967.1(SAMD13):​c.70-4847A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.422 in 151,924 control chromosomes in the GnomAD database, including 14,973 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 0.42 (14973 hom., cov: 31)
• Consequence: SAMD13 ENST00000454967.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.152

Genes affected

SAMD13 (HGNC:24582): (sterile alpha motif domain containing 13) Predicted to enable chromatin binding activity and histone binding activity. Predicted to be involved in negative regulation of transcription, DNA-templated. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

UOX (HGNC:12575): (urate oxidase (pseudogene)) Urate oxidase is an enzyme that catalyzes the oxidation of uric acid to allantoin. This gene has been inactivated by mutation and is nonfunctional in humans and some other primates. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.515 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UOX	NR_003927.2	n.209+1160T>A		intron_variant	Intron 1 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SAMD13	ENST00000454967.1	c.70-4847A>T		intron_variant	Intron 1 of 2	3		ENSP00000391978.1
UOX	ENST00000471089.6	n.249+1160T>A		intron_variant	Intron 2 of 7	6
UOX	ENST00000483236.2	n.209+1160T>A		intron_variant	Intron 1 of 4	5

Frequencies

GnomAD3 genomes AF: 0.423 AC: 64143 AN: 151806 Hom.: 14962 Cov.: 31

Gnomad AFR AF: 0.222

Gnomad AMI AF: 0.386

Gnomad AMR AF: 0.469

Gnomad ASJ AF: 0.535

Gnomad EAS AF: 0.445

Gnomad SAS AF: 0.415

Gnomad FIN AF: 0.470

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.519

Gnomad OTH AF: 0.451

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

GnomAD4 genome AF: 0.422 AC: 64167 AN: 151924 Hom.: 14973 Cov.: 31 AF XY: 0.421 AC XY: 31227 AN XY: 74226

Gnomad4 AFR AF: 0.222

Gnomad4 AMR AF: 0.469

Gnomad4 ASJ AF: 0.535

Gnomad4 EAS AF: 0.445

Gnomad4 SAS AF: 0.417

Gnomad4 FIN AF: 0.470

Gnomad4 NFE AF: 0.519

Gnomad4 OTH AF: 0.454

Alfa AF: 0.451 Hom.: 2015

Bravo AF: 0.416

Asia WGS AF: 0.391 AC: 1361 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.0
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs315511; hg19: chr1-84849116;