rs315537

Variant names:

• chr1-84352910-A-T
• rs315537
• ENST00000454967.1:c.69+27162A>T

Variant summary

Our verdict is Benign. The variant received -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
• 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]

ACMG classification

Our verdict: Benign. The variant received -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.

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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SAMD13	ENST00000454967.1	TSL:3	c.69+27162A>T		intron	N/A	ENSP00000391978.1	H7BZX5

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

African (AFR) AF: 0.275 AC: 11414 AN: 41450

American (AMR) AF: 0.295 AC: 4505 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.467 AC: 1621 AN: 3468

East Asian (EAS) AF: 0.243 AC: 1255 AN: 5170

South Asian (SAS) AF: 0.358 AC: 1727 AN: 4824

European-Finnish (FIN) AF: 0.417 AC: 4398 AN: 10554

Middle Eastern (MID) AF: 0.432 AC: 126 AN: 292

European-Non Finnish (NFE) AF: 0.402 AC: 27293 AN: 67968

Other (OTH) AF: 0.346 AC: 732 AN: 2114

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.5
DANN	Benign	0.76
PhyloP100		0.54

Splicing

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

Other links and lift over

dbSNP: rs315537; hg19: chr1-84818593;