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. The variant received -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
• Publications: 3 publications found

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]

ENSG00000293446 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000454967.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UOX	NR_003927.2		n.209+1160T>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SAMD13	ENST00000454967.1	TSL:3	c.70-4847A>T		intron	N/A	ENSP00000391978.1	H7BZX5
	UOX	ENST00000471089.6	TSL:6	n.249+1160T>A		intron	N/A
	ENSG00000293446	ENST00000483236.2	TSL:5	n.209+1160T>A		intron	N/A

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

African (AFR) AF: 0.222 AC: 9185 AN: 41454

American (AMR) AF: 0.469 AC: 7148 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.535 AC: 1856 AN: 3468

East Asian (EAS) AF: 0.445 AC: 2296 AN: 5154

South Asian (SAS) AF: 0.417 AC: 2009 AN: 4820

European-Finnish (FIN) AF: 0.470 AC: 4943 AN: 10524

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.519 AC: 35285 AN: 67934

Other (OTH) AF: 0.454 AC: 960 AN: 2116

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.0
DANN	Benign	0.78
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs315511; hg19: chr1-84849116;