rs12118313

Variant names:

• chr1-161068189-C-A
• rs12118313
• NM_001025598.2:c.97+1339G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001025598.2(ARHGAP30):​c.97+1339G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.786 in 152,128 control chromosomes in the GnomAD database, including 47,197 homozygotes. 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: 𝑓 0.79 (47197 hom., cov: 32)
• Consequence: ARHGAP30 NM_001025598.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00900
• Publications: 6 publications found

Genes affected

ARHGAP30 (HGNC:27414): (Rho GTPase activating protein 30) Predicted to enable GTPase activator activity. Predicted to be involved in small GTPase mediated signal transduction. Located in intracellular membrane-bounded organelle. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.845 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ARHGAP30	NM_001025598.2	c.97+1339G>T		intron_variant	Intron 1 of 11	ENST00000368013.8	NP_001020769.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ARHGAP30	ENST00000368013.8	c.97+1339G>T		intron_variant	Intron 1 of 11	2	NM_001025598.2	ENSP00000356992.3

Frequencies

GnomAD3 genomes AF: 0.786 AC: 119447 AN: 152010 Hom.: 47152 Cov.: 32

Gnomad AFR AF: 0.852

Gnomad AMI AF: 0.804

Gnomad AMR AF: 0.728

Gnomad ASJ AF: 0.815

Gnomad EAS AF: 0.664

Gnomad SAS AF: 0.725

Gnomad FIN AF: 0.762

Gnomad MID AF: 0.783

Gnomad NFE AF: 0.774

Gnomad OTH AF: 0.789

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

GnomAD4 genome AF: 0.786 AC: 119551 AN: 152128 Hom.: 47197 Cov.: 32 AF XY: 0.781 AC XY: 58096 AN XY: 74366

African (AFR) AF: 0.852 AC: 35384 AN: 41514

American (AMR) AF: 0.728 AC: 11122 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.815 AC: 2828 AN: 3470

East Asian (EAS) AF: 0.665 AC: 3437 AN: 5170

South Asian (SAS) AF: 0.724 AC: 3488 AN: 4818

European-Finnish (FIN) AF: 0.762 AC: 8070 AN: 10590

Middle Eastern (MID) AF: 0.784 AC: 229 AN: 292

European-Non Finnish (NFE) AF: 0.774 AC: 52588 AN: 67976

Other (OTH) AF: 0.792 AC: 1672 AN: 2112

Alfa AF: 0.779 Hom.: 58282

Bravo AF: 0.789

Asia WGS AF: 0.683 AC: 2378 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.1
DANN	Benign	0.72
PhyloP100		-0.0090
Mutation Taster		=100/0	polymorphism (auto)

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: rs12118313; hg19: chr1-161037979;