NM_022733.3:c.403-180C>G

Variant names:

• chr1-40412836-C-G
• rs209603
• NM_022733.3:c.403-180C>G

Variant summary

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

The NM_022733.3(SMAP2):​c.403-180C>G 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: 30)
• Consequence: SMAP2 NM_022733.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.352
• Publications: 2 publications found

Genes affected

SMAP2 (HGNC:25082): (small ArfGAP2) Predicted to enable GTPase activator activity. Predicted to be involved in regulation of catalytic activity. Predicted to be located in cytoplasm. [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=-0.82).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_022733.3. 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
	SMAP2	NM_022733.3	MANE Select	c.403-180C>G		intron	N/A	NP_073570.1
	SMAP2	NM_001198979.2		c.388-180C>G		intron	N/A	NP_001185908.1
	SMAP2	NM_001198978.2		c.313-180C>G		intron	N/A	NP_001185907.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SMAP2	ENST00000372718.8	TSL:1 MANE Select	c.403-180C>G		intron	N/A	ENSP00000361803.3
	SMAP2	ENST00000614549.4	TSL:1	c.388-180C>G		intron	N/A	ENSP00000479285.1
	SMAP2	ENST00000372708.5	TSL:1	c.313-180C>G		intron	N/A	ENSP00000361793.1

Frequencies

GnomAD3 genomes Cov.: 30

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

GnomAD4 genome Cov.: 30

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.67
DANN	Benign	0.52
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs209603; hg19: chr1-40878508; COSMIC: COSV65532764; COSMIC: COSV65532764;