X-111251300-GAAA-GAAAAAA

Variant names:

• chrX-111251300-G-GAAA
• rs201147886
• NM_014289.4:c.894-17_894-15dupTTT

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The NM_014289.4(CAPN6):​c.894-17_894-15dupTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 18)
  • Exomes 𝑓: 0.000027 (0 hom. 0 hem.)
• Consequence: CAPN6 NM_014289.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.31

Genes affected

CAPN6 (HGNC:1483): (calpain 6) Calpains are ubiquitous, well-conserved family of calcium-dependent, cysteine proteases. The calpain proteins are heterodimers consisting of an invariant small subunit and variable large subunits. The large subunit possesses a cysteine protease domain, and both subunits possess calcium-binding domains. Calpains have been implicated in neurodegenerative processes, as their activation can be triggered by calcium influx and oxidative stress. The protein encoded by this gene is highly expressed in the placenta. Its C-terminal region lacks any homology to the calmodulin-like domain of other calpains. The protein lacks critical active site residues and thus is suggested to be proteolytically inactive. The protein may play a role in tumor formation by inhibiting apoptosis and promoting angiogenesis. [provided by RefSeq, Nov 2009]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CAPN6	NM_014289.4	c.894-17_894-15dupTTT		intron_variant	Intron 6 of 12	ENST00000324068.2	NP_055104.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CAPN6	ENST00000324068.2	c.894-15_894-14insTTT		intron_variant	Intron 6 of 12	1	NM_014289.4	ENSP00000317214.1

Frequencies

GnomAD3 genomes Cov.: 18

GnomAD3 exomes AF: 0.000111 AC: 5 AN: 45184 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2042

Gnomad AFR exome AF: 0.000192

Gnomad AMR exome AF: 0.000143

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.000328

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000517

Gnomad OTH exome AF: 0.000889

GnomAD4 exome AF: 0.0000273 AC: 23 AN: 840992 Hom.: 0 Cov.: 10 AF XY: 0.00 AC XY: 0 AN XY: 253836

Gnomad4 AFR exome AF: 0.000300

Gnomad4 AMR exome AF: 0.0000446

Gnomad4 ASJ exome AF: 0.000130

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000256

Gnomad4 FIN exome AF: 0.0000597

Gnomad4 NFE exome AF: 0.0000170

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 18

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: rs201147886; hg19: chrX-110494528;