rs1933633

chr1-230788630-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_006615.3(CAPN9):c.1599+1028G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.168 in 152,168 control chromosomes in the GnomAD database, including 2,265 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 0.17 (2265 hom., cov: 32)
• Consequence: CAPN9 NM_006615.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0880

Genes affected

CAPN9 (HGNC:1486): (calpain 9) 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 expressed predominantly in stomach and small intestine and may have specialized functions in the digestive tract. This gene is thought to be associated with gastric cancer. Multiple alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.19 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CAPN9	NM_006615.3	c.1599+1028G>A		intron_variant		ENST00000271971.7
LOC107985359	XR_001738518.2	n.99+6483C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CAPN9	ENST00000271971.7	c.1599+1028G>A		intron_variant		1	NM_006615.3	P1
	ENST00000412344.1	n.380+6483C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.168 AC: 25504 AN: 152050 Hom.: 2265 Cov.: 32

Gnomad AFR AF: 0.137

Gnomad AMI AF: 0.154

Gnomad AMR AF: 0.151

Gnomad ASJ AF: 0.221

Gnomad EAS AF: 0.0831

Gnomad SAS AF: 0.200

Gnomad FIN AF: 0.196

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.187

Gnomad OTH AF: 0.185

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

GnomAD4 genome AF: 0.168 AC: 25521 AN: 152168 Hom.: 2265 Cov.: 32 AF XY: 0.167 AC XY: 12408 AN XY: 74382

Gnomad4 AFR AF: 0.137

Gnomad4 AMR AF: 0.151

Gnomad4 ASJ AF: 0.221

Gnomad4 EAS AF: 0.0829

Gnomad4 SAS AF: 0.200

Gnomad4 FIN AF: 0.196

Gnomad4 NFE AF: 0.187

Gnomad4 OTH AF: 0.183

Alfa AF: 0.189 Hom.: 3719

Bravo AF: 0.163

Asia WGS AF: 0.140 AC: 488 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	1.6
Dann	Benign	0.74

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

Publications

LitVar

Other links and lift over

dbSNP: rs1933633; hg19: chr1-230924376;