rs1029077

Variant names:

• chr10-31808878-A-C
• rs1029077
• NM_018287.7:c.2263+116T>G

Your query was ambiguous. Multiple possible variants found:

• chr10-31808878-A-C
• chr10-31808878-A-T

Variant summary

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

The NM_018287.7(ARHGAP12):​c.2263+116T>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: 33)
• Consequence: ARHGAP12 NM_018287.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.23
• Publications: 2 publications found

Genes affected

ARHGAP12 (HGNC:16348): (Rho GTPase activating protein 12) This gene encodes a member of a large family of proteins that activate Rho-type guanosine triphosphate (GTP) metabolizing enzymes. The encoded protein may be involved in suppressing tumor formation by regulating cell invasion and adhesion. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Jul 2012]

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=-0.81).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018287.7. 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
	ARHGAP12	NM_018287.7	MANE Select	c.2263+116T>G		intron	N/A	NP_060757.4
	ARHGAP12	NM_001270695.1		c.2248+116T>G		intron	N/A	NP_001257624.1
	ARHGAP12	NM_001270696.2		c.2173+116T>G		intron	N/A	NP_001257625.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ARHGAP12	ENST00000344936.7	TSL:1 MANE Select	c.2263+116T>G		intron	N/A	ENSP00000345808.2
	ARHGAP12	ENST00000396144.8	TSL:1	c.2248+116T>G		intron	N/A	ENSP00000379448.4
	ARHGAP12	ENST00000375250.9	TSL:1	c.2173+116T>G		intron	N/A	ENSP00000364399.5

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 17

GnomAD4 genome Cov.: 33

Alfa AF: 0.00 Hom.: 126

Bravo AF: 0.0000113

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	8.8
DANN	Benign	0.72
PhyloP100		3.2

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: rs1029077; hg19: chr10-32097806;