1-84383433-A-T

Position:

• chr1-84383433-A-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:):

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/exons	MANE	Protein	UniProt
UOX	NR_003927.2	n.209+1160T>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SAMD13	ENST00000454967.1	c.70-4847A>T		intron_variant		3		ENSP00000391978.1
UOX	ENST00000471089.6	n.249+1160T>A		intron_variant		6
UOX	ENST00000483236.2	n.209+1160T>A		intron_variant		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;