rs79888638

Variant names:

• chr3-151880738-C-A
• rs79888638
• NM_033050.6:c.195C>A

Your query was ambiguous. Multiple possible variants found:

• chr3-151880738-C-A
• chr3-151880738-C-G
• chr3-151880738-C-T

Variant summary

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

The NM_033050.6(SUCNR1):​c.195C>A​(p.Leu65Leu) 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. Synonymous variant affecting the same amino acid position (i.e. L65L) has been classified as Benign.

• Frequency: Genomes: not found (cov: 32)
• Consequence: SUCNR1 NM_033050.6 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.367
• Publications: 3 publications found

Genes affected

SUCNR1 (HGNC:4542): (succinate receptor 1) This gene encodes a G-protein-coupled receptor for succinate, an intermediate molecule of the citric acid cycle. It is involved in the promotion of hematopoietic progenitor cell development, and it has a potential role in renovascular hypertension which has known correlations to renal failure, diabetes and atherosclerosis. [provided by RefSeq, Oct 2009]

AADACL2-AS1 (HGNC:50301): (AADACL2 antisense RNA 1)

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=-0.34).
• BP7: Synonymous conserved (PhyloP=-0.367 with no splicing effect.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_033050.6. 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
	SUCNR1	NM_033050.6	MANE Select	c.195C>A	p.Leu65Leu	synonymous	Exon 3 of 3	NP_149039.2
	AADACL2-AS1	NR_110202.1		n.319+47119G>T		intron	N/A
	AADACL2-AS1	NR_110203.1		n.319+47119G>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SUCNR1	ENST00000362032.6	TSL:1 MANE Select	c.195C>A	p.Leu65Leu	synonymous	Exon 3 of 3	ENSP00000355156.4	Q9BXA5
	SUCNR1	ENST00000875328.1		c.195C>A	p.Leu65Leu	synonymous	Exon 2 of 2	ENSP00000545387.1
	SUCNR1	ENST00000943239.1		c.195C>A	p.Leu65Leu	synonymous	Exon 3 of 3	ENSP00000613298.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 1

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.34
CADD	Benign	2.8
DANN	Benign	0.75
PhyloP100		-0.37

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: rs79888638; hg19: chr3-151598526;