6-130184126-G-A

Variant names:

• chr6-130184126-G-A
• rs144450186
• NM_001017373.4:c.631C>T

Variant summary

Our verdict is Likely benign. The variant received -1 ACMG points: 2P and 3B. PM2 BP4_Moderate BP7

The NM_001017373.4(SAMD3):​c.631C>T​(p.Leu211Leu) variant causes a synonymous 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: SAMD3 NM_001017373.4 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.40
• Publications: 0 publications found

Genes affected

SAMD3 (HGNC:21574): (sterile alpha motif domain containing 3)

ACMG classification

Our verdict: Likely_benign. The variant received -1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.43).
• BP7: Synonymous conserved (PhyloP=2.4 with no splicing effect.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001017373.4. 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
	SAMD3	NM_001017373.4	MANE Select	c.631C>T	p.Leu211Leu	synonymous	Exon 7 of 12	NP_001017373.2	Q8N6K7-1
	SAMD3	NM_001277185.2		c.703C>T	p.Leu235Leu	synonymous	Exon 6 of 11	NP_001264114.1	Q8N6K7-3
	SAMD3	NM_001258275.3		c.631C>T	p.Leu211Leu	synonymous	Exon 9 of 14	NP_001245204.1	Q8N6K7-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SAMD3	ENST00000439090.7	TSL:2 MANE Select	c.631C>T	p.Leu211Leu	synonymous	Exon 7 of 12	ENSP00000403565.2	Q8N6K7-1
	SAMD3	ENST00000324172.10	TSL:1	c.631C>T	p.Leu211Leu	synonymous	Exon 5 of 6	ENSP00000324874.6	Q8N6K7-2
	SAMD3	ENST00000524930.1	TSL:1	n.*515C>T		non_coding_transcript_exon	Exon 5 of 6	ENSP00000436997.1	E9PPN0

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD2 exomes AF: 0.00000398 AC: 1 AN: 251342 AF XY: 0.00000736

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00000880

Gnomad OTH exome AF: 0.00

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.43
CADD	Benign	9.0
DANN	Benign	0.82
PhyloP100		2.4

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs144450186; hg19: chr6-130505271;