5-151287372-C-G

Variant names:

• chr5-151287372-C-G
• rs375396
• NM_181774.4:c.582G>C

Variant summary

Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2 BP4_Strong BP7

The NM_001145017.2(SLC36A3):​c.705G>C​(p.Leu235Leu) 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: 31)
• Consequence: SLC36A3 NM_001145017.2 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.374
• Publications: 18 publications found

Genes affected

SLC36A3 (HGNC:19659): (solute carrier family 36 member 3) Predicted to enable amino acid transmembrane transporter activity. Predicted to be involved in amino acid transport and proton transmembrane transport. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Likely_benign. The variant received -3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BP7: Synonymous conserved (PhyloP=-0.374 with no splicing effect.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001145017.2. 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
	SLC36A3	NM_181774.4	MANE Select	c.582G>C	p.Leu194Leu	synonymous	Exon 6 of 10	NP_861439.3
	SLC36A3	NM_001145017.2		c.705G>C	p.Leu235Leu	synonymous	Exon 7 of 11	NP_001138489.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC36A3	ENST00000335230.8	TSL:1 MANE Select	c.582G>C	p.Leu194Leu	synonymous	Exon 6 of 10	ENSP00000334750.3
	SLC36A3	ENST00000377713.3	TSL:1	c.705G>C	p.Leu235Leu	synonymous	Exon 7 of 11	ENSP00000366942.3
	SLC36A3	ENST00000423071.2	TSL:2	n.2482G>C		non_coding_transcript_exon	Exon 5 of 9

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Cov.: 51

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	5.6
DANN	Benign	0.68
PhyloP100		-0.37

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: rs375396; hg19: chr5-150666933;