NM_001134663.2:c.165+1542G>A

Variant names:

• chr1-84327290-G-A
• rs315553
• NM_001134663.2:c.165+1542G>A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001134663.2(SAMD13):​c.165+1542G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: SAMD13 NM_001134663.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.165
• 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]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001134663.2. 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
	SAMD13	NM_001134663.2	MANE Select	c.165+1542G>A		intron	N/A	NP_001128135.1	Q5VXD3-4
	SAMD13	NM_001010971.3		c.207+1542G>A		intron	N/A	NP_001010971.1	Q5VXD3-2
	SAMD13	NM_001134664.2		c.165+1542G>A		intron	N/A	NP_001128136.1	Q5VXD3-4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SAMD13	ENST00000394834.8	TSL:2 MANE Select	c.165+1542G>A		intron	N/A	ENSP00000378311.3	Q5VXD3-4
	SAMD13	ENST00000370668.7	TSL:1	c.165+1542G>A		intron	N/A	ENSP00000359702.3	Q5VXD3-4
	SAMD13	ENST00000370671.7	TSL:3	c.225+1542G>A		intron	N/A	ENSP00000359705.3	Q5VXD3-1

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.1
DANN	Benign	0.46
PhyloP100		0.17

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs315553; hg19: chr1-84792973;