rs315537

chr1-84352910-A-T

Variant summary

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

The ENST00000454967.1(SAMD13):c.69+27162A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.351 in 152,020 control chromosomes in the GnomAD database, including 9,798 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 0.35 (9798 hom., cov: 32)
• Consequence: SAMD13 ENST00000454967.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.537

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.398 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SAMD13	ENST00000454967.1	c.69+27162A>T		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.352 AC: 53395 AN: 151902 Hom.: 9800 Cov.: 32

Gnomad AFR AF: 0.275

Gnomad AMI AF: 0.366

Gnomad AMR AF: 0.295

Gnomad ASJ AF: 0.467

Gnomad EAS AF: 0.243

Gnomad SAS AF: 0.359

Gnomad FIN AF: 0.417

Gnomad MID AF: 0.433

Gnomad NFE AF: 0.402

Gnomad OTH AF: 0.348

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

GnomAD4 genome AF: 0.351 AC: 53405 AN: 152020 Hom.: 9798 Cov.: 32 AF XY: 0.351 AC XY: 26086 AN XY: 74310

Gnomad4 AFR AF: 0.275

Gnomad4 AMR AF: 0.295

Gnomad4 ASJ AF: 0.467

Gnomad4 EAS AF: 0.243

Gnomad4 SAS AF: 0.358

Gnomad4 FIN AF: 0.417

Gnomad4 NFE AF: 0.402

Gnomad4 OTH AF: 0.346

Alfa AF: 0.382 Hom.: 1563

Bravo AF: 0.339

Asia WGS AF: 0.285 AC: 993 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	6.5
Dann	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs315537; hg19: chr1-84818593;