rs2242436

Variant names:

• chr19-1065946-C-A
• rs2242436
• ENST00000539243.6:c.-80C>A

Your query was ambiguous. Multiple possible variants found:

• chr19-1065946-C-A
• chr19-1065946-C-G
• chr19-1065946-C-T

Variant summary

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

The ENST00000539243.6(ARHGAP45):​c.-80C>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000751 in 1,331,908 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: 34)
  • Exomes 𝑓: 7.5e-7 (0 hom.)
• Consequence: ARHGAP45 ENST00000539243.6 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.26
• Publications: 15 publications found

Genes affected

ARHGAP45 (HGNC:17102): (Rho GTPase activating protein 45) Predicted to enable GTPase activator activity. Predicted to be involved in activation of GTPase activity. Located in membrane. [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=-0.92).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000539243.6. 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
	ARHGAP45	NM_001258328.4		c.-80C>A		upstream_gene	N/A	NP_001245257.1	Q92619-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ARHGAP45	ENST00000539243.6	TSL:2	c.-80C>A		5_prime_UTR	Exon 1 of 23	ENSP00000439601.1	Q92619-2

Frequencies

GnomAD3 genomes Cov.: 34

GnomAD4 exome AF: 7.51e-7 AC: 1 AN: 1331908 Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0 AN XY: 651986

African (AFR) AF: 0.00 AC: 0 AN: 30142

American (AMR) AF: 0.00 AC: 0 AN: 29574

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 21706

East Asian (EAS) AF: 0.00 AC: 0 AN: 35326

South Asian (SAS) AF: 0.00 AC: 0 AN: 71612

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 31562

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3896

European-Non Finnish (NFE) AF: 9.50e-7 AC: 1 AN: 1052602

Other (OTH) AF: 0.00 AC: 0 AN: 55488

GnomAD4 genome Cov.: 34

Alfa AF: 0.00 Hom.: 4201

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.11
DANN	Benign	0.38
PhyloP100		-4.3
PromoterAI		-0.10	Neutral

Splicing

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

Other links and lift over

dbSNP: rs2242436; hg19: chr19-1065945;