rs10542660

Variant names:

• chrX-63637846-CTGTGTGTGTGTGTG-C
• rs10542660
• NM_001353921.2:c.*168_*181delCACACACACACACA

Your query was ambiguous. Multiple possible variants found:

• chrX-63637846-CTGTGTGTGTGTGTG-C
• chrX-63637846-CTGTGTGTGTGTGTG-CTG
• chrX-63637846-CTGTGTGTGTGTGTG-CTGTG
• chrX-63637846-CTGTGTGTGTGTGTG-CTGTGTG
• chrX-63637846-CTGTGTGTGTGTGTG-CTGTGTGTG
• chrX-63637846-CTGTGTGTGTGTGTG-CTGTGTGTGTG
• chrX-63637846-CTGTGTGTGTGTGTG-CTGTGTGTGTGTG
• chrX-63637846-CTGTGTGTGTGTGTG-CTGTGTGTGTGTGTGTG
• chrX-63637846-CTGTGTGTGTGTGTG-CTGTGTGTGTGTGTGTGTG
• chrX-63637846-CTGTGTGTGTGTGTG-CTGTGTGTGTGTGTGTGTGTG
• chrX-63637846-CTGTGTGTGTGTGTG-CTGTGTGTGTGTGTGTGTGTGTGTG
• chrX-63637846-CTGTGTGTGTGTGTG-CTGTGTGTGTGTGTGTGTGTGTGTGTGTG

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2

The NM_001353921.2(ARHGEF9):​c.*168_*181delCACACACACACACA variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000386 in 310,520 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 5 hemizygotes in GnomAD. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.000021 (0 hom., 1 hem., cov: 12)
  • Exomes 𝑓: 0.000047 (0 hom. 4 hem.)
• Consequence: ARHGEF9 NM_001353921.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.56

Genes affected

ARHGEF9 (HGNC:14561): (Cdc42 guanine nucleotide exchange factor 9) The protein encoded by this gene is a Rho-like GTPase that switches between the active (GTP-bound) state and inactive (GDP-bound) state to regulate CDC42 and other genes. This brain-specific protein also acts as an adaptor protein for the recruitment of gephyrin and together these proteins facilitate receceptor recruitement in GABAnergic and glycinergic synapses. Defects in this gene are the cause of startle disease with epilepsy (STHEE), also known as hyperekplexia with epilepsy, as well as several other types of cognitive disability. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2017]

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BS2: High Hemizygotes in GnomAdExome4 at 4 XL gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ARHGEF9	NM_001353921.2	c.*168_*181delCACACACACACACA		3_prime_UTR_variant	Exon 10 of 10	ENST00000671741.2	NP_001340850.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ARHGEF9	ENST00000671741	c.*168_*181delCACACACACACACA		3_prime_UTR_variant	Exon 10 of 10		NM_001353921.2	ENSP00000500715.1

Frequencies

GnomAD3 genomes AF: 0.0000309 AC: 3 AN: 97025 Hom.: 0 Cov.: 12 AF XY: 0.0000842 AC XY: 2 AN XY: 23765

Gnomad AFR AF: 0.0000777

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000318

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.0000468 AC: 10 AN: 213481 Hom.: 0 AF XY: 0.0000628 AC XY: 4 AN XY: 63651

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.000405

Gnomad4 SAS exome AF: 0.000132

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0000145

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0000206 AC: 2 AN: 97039 Hom.: 0 Cov.: 12 AF XY: 0.0000420 AC XY: 1 AN XY: 23789

Gnomad4 AFR AF: 0.0000776

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00

Gnomad4 OTH AF: 0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10542660; hg19: chrX-62857726;