rs1326391621

Variant names:

• chr11-66017182-T-C
• NM_053054.4:c.2202-8A>G

Your query was ambiguous. Multiple possible variants found:

• chr11-66017182-T-C
• chr11-66017182-T-G

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The NM_053054.4(CATSPER1):​c.2202-8A>G variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 0)
  • Exomes 𝑓: 0.0000061 (0 hom.)
• Consequence: CATSPER1 NM_053054.4 splice_region, intron
• Scores: Splicing: ADA: 0.000007049
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.09

Genes affected

CATSPER1 (HGNC:17116): (cation channel sperm associated 1) Calcium ions play a primary role in the regulation of sperm motility. This gene belongs to a family of putative cation channels that are specific to spermatozoa and localize to the flagellum. The protein family features a single repeat with six membrane-spanning segments and a predicted calcium-selective pore region. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CATSPER1	NM_053054.4	c.2202-8A>G		splice_region_variant, intron_variant	Intron 10 of 11	ENST00000312106.6	NP_444282.3
CATSPER1	XM_047426337.1	c.*36-8A>G		splice_region_variant, intron_variant	Intron 10 of 10		XP_047282293.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CATSPER1	ENST00000312106.6	c.2202-8A>G		splice_region_variant, intron_variant	Intron 10 of 11	1	NM_053054.4	ENSP00000309052.5
CATSPER1	ENST00000529244.1	n.442-8A>G		splice_region_variant, intron_variant	Intron 4 of 5	3

Frequencies

GnomAD3 genomes Cov.: 0

GnomAD4 exome AF: 0.00000608 AC: 1 AN: 164388 Hom.: 0 Cov.: 0 AF XY: 0.0000105 AC XY: 1 AN XY: 95038

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0000113

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.18
DANN	Benign	0.36

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Benign	0.0000070
dbscSNV1_RF	Benign	0.0
SpliceAI score (max)		0.090		Details are displayed if max score is > 0.2

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr11-65784653;