rs17478556

Variant names:

• chr1-84386440-G-C
• rs17478556
• ENST00000454967.1:c.70-1840G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000454967.1(SAMD13):​c.70-1840G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0295 in 152,312 control chromosomes in the GnomAD database, including 88 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 0.030 (88 hom., cov: 32)
• Consequence: SAMD13 ENST00000454967.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.513
• Publications: 0 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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BS1: Variant frequency is greater than expected in population sas. GnomAd4 allele frequency = 0.0295 (4495/152312) while in subpopulation SAS AF = 0.0386 (186/4816). AF 95% confidence interval is 0.0341. There are 88 homozygotes in GnomAd4. There are 2191 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 88 AR gene

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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SAMD13	ENST00000454967.1	TSL:3	c.70-1840G>C		intron	N/A	ENSP00000391978.1
	UOX	ENST00000471089.6	TSL:6	n.31-1629C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0295 AC: 4493 AN: 152194 Hom.: 87 Cov.: 32

Gnomad AFR AF: 0.0216

Gnomad AMI AF: 0.0208

Gnomad AMR AF: 0.0350

Gnomad ASJ AF: 0.0726

Gnomad EAS AF: 0.00982

Gnomad SAS AF: 0.0386

Gnomad FIN AF: 0.0127

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0344

Gnomad OTH AF: 0.0315

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

GnomAD4 genome AF: 0.0295 AC: 4495 AN: 152312 Hom.: 88 Cov.: 32 AF XY: 0.0294 AC XY: 2191 AN XY: 74472

African (AFR) AF: 0.0216 AC: 897 AN: 41568

American (AMR) AF: 0.0348 AC: 533 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0726 AC: 252 AN: 3472

East Asian (EAS) AF: 0.0100 AC: 52 AN: 5180

South Asian (SAS) AF: 0.0386 AC: 186 AN: 4816

European-Finnish (FIN) AF: 0.0127 AC: 135 AN: 10624

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0344 AC: 2338 AN: 68032

Other (OTH) AF: 0.0312 AC: 66 AN: 2116

Alfa AF: 0.0293 Hom.: 15

Bravo AF: 0.0302

Asia WGS AF: 0.0210 AC: 76 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.8
DANN	Benign	0.81
PhyloP100		0.51

Splicing

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

Other links and lift over

dbSNP: rs17478556; hg19: chr1-84852123;