1-84327290-G-T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001134663.2(SAMD13):​c.165+1542G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.84 in 152,096 control chromosomes in the GnomAD database, including 55,170 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 0.84 (55170 hom., cov: 32)
• Consequence: SAMD13 NM_001134663.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.165
• Publications: 5 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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.951 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SAMD13	NM_001134663.2	c.165+1542G>T		intron_variant	Intron 3 of 3	ENST00000394834.8	NP_001128135.1
SAMD13	NM_001010971.3	c.207+1542G>T		intron_variant	Intron 3 of 3		NP_001010971.1
SAMD13	NM_001134664.2	c.165+1542G>T		intron_variant	Intron 3 of 3		NP_001128136.1
SAMD13	XM_017000377.3	c.225+1542G>T		intron_variant	Intron 3 of 3		XP_016855866.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SAMD13	ENST00000394834.8	c.165+1542G>T		intron_variant	Intron 3 of 3	2	NM_001134663.2	ENSP00000378311.3

Frequencies

GnomAD3 genomes AF: 0.840 AC: 127644 AN: 151978 Hom.: 55150 Cov.: 32

Gnomad AFR AF: 0.618

Gnomad AMI AF: 0.992

Gnomad AMR AF: 0.835

Gnomad ASJ AF: 0.957

Gnomad EAS AF: 0.854

Gnomad SAS AF: 0.863

Gnomad FIN AF: 0.884

Gnomad MID AF: 0.911

Gnomad NFE AF: 0.957

Gnomad OTH AF: 0.861

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

GnomAD4 genome AF: 0.840 AC: 127705 AN: 152096 Hom.: 55170 Cov.: 32 AF XY: 0.837 AC XY: 62211 AN XY: 74366

African (AFR) AF: 0.618 AC: 25612 AN: 41410

American (AMR) AF: 0.835 AC: 12750 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.957 AC: 3320 AN: 3468

East Asian (EAS) AF: 0.854 AC: 4420 AN: 5174

South Asian (SAS) AF: 0.864 AC: 4166 AN: 4824

European-Finnish (FIN) AF: 0.884 AC: 9363 AN: 10590

Middle Eastern (MID) AF: 0.908 AC: 267 AN: 294

European-Non Finnish (NFE) AF: 0.957 AC: 65098 AN: 68036

Other (OTH) AF: 0.855 AC: 1804 AN: 2110

Alfa AF: 0.902 Hom.: 105758

Bravo AF: 0.828

Asia WGS AF: 0.836 AC: 2906 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.2
DANN	Benign	0.39
PhyloP100		0.17
Mutation Taster		=100/0	polymorphism (auto)

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;