rs2915776

Variant names:

• chr15-43630388-T-C
• rs2915776
• NM_172095.4:c.*313A>G

Your query was ambiguous. Multiple possible variants found:

• chr15-43630388-T-C
• chr15-43630388-T-A

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_172095.4(CATSPER2):​c.*313A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.163 in 409,544 control chromosomes in the GnomAD database, including 9,069 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.21 (5540 hom., cov: 31)
  • Exomes 𝑓: 0.13 (3529 hom.)
• Consequence: CATSPER2 NM_172095.4 3_prime_UTR
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 0.302
• Publications: 2 publications found

Genes affected

CATSPER2 (HGNC:18810): (cation channel sperm associated 2) This gene encodes a member of a family of cation channel proteins that localize to the flagellum of spermatozoa. Defects at this locus causes male infertility. Alternatively spliced transcript variants have been observed at this locus. Readthrough transcription originates upstream of this locus in diphosphoinositol pentakisphosphate kinase 1 pseudogene 1 and is represented by GeneID:110006325. Related pseudogenes are found next to this locus on chromosome 15 and on chromosome 5. [provided by RefSeq, Mar 2017]

ENSG00000284772 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BP6: Variant 15-43630388-T-C is Benign according to our data. Variant chr15-43630388-T-C is described in ClinVar as Benign. ClinVar VariationId is 1290268.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.456 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_172095.4. 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
	CATSPER2	NM_172095.4	MANE Select	c.*313A>G		3_prime_UTR	Exon 13 of 13	NP_742093.1	Q96P56-1
	CATSPER2	NM_001282309.3		c.*313A>G		3_prime_UTR	Exon 14 of 14	NP_001269238.1	Q96P56-2
	CATSPER2	NM_001282310.2		c.*313A>G		downstream_gene	N/A	NP_001269239.1	F8W9H2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CATSPER2	ENST00000396879.8	TSL:2 MANE Select	c.*313A>G		3_prime_UTR	Exon 13 of 13	ENSP00000380088.3	Q96P56-1
	ENSG00000284772	ENST00000643290.1		n.85+1811A>G		intron	N/A	ENSP00000495476.1	A0A2R8Y6Q2
	ENSG00000309475	ENST00000841330.1		n.457-1845T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.213 AC: 32218 AN: 151560 Hom.: 5524 Cov.: 31

Gnomad AFR AF: 0.461

Gnomad AMI AF: 0.107

Gnomad AMR AF: 0.193

Gnomad ASJ AF: 0.182

Gnomad EAS AF: 0.277

Gnomad SAS AF: 0.196

Gnomad FIN AF: 0.0398

Gnomad MID AF: 0.162

Gnomad NFE AF: 0.0935

Gnomad OTH AF: 0.187

GnomAD4 exome AF: 0.134 AC: 34655 AN: 257866 Hom.: 3529 Cov.: 3 AF XY: 0.137 AC XY: 19327 AN XY: 140914

African (AFR) AF: 0.470 AC: 3360 AN: 7152

American (AMR) AF: 0.193 AC: 2472 AN: 12780

Ashkenazi Jewish (ASJ) AF: 0.190 AC: 1237 AN: 6520

East Asian (EAS) AF: 0.279 AC: 3440 AN: 12340

South Asian (SAS) AF: 0.180 AC: 7544 AN: 41818

European-Finnish (FIN) AF: 0.0410 AC: 515 AN: 12546

Middle Eastern (MID) AF: 0.135 AC: 135 AN: 1000

European-Non Finnish (NFE) AF: 0.0939 AC: 14117 AN: 150340

Other (OTH) AF: 0.137 AC: 1835 AN: 13370

GnomAD4 genome AF: 0.213 AC: 32280 AN: 151678 Hom.: 5540 Cov.: 31 AF XY: 0.210 AC XY: 15547 AN XY: 74132

African (AFR) AF: 0.461 AC: 19028 AN: 41266

American (AMR) AF: 0.193 AC: 2937 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.182 AC: 631 AN: 3462

East Asian (EAS) AF: 0.277 AC: 1425 AN: 5142

South Asian (SAS) AF: 0.196 AC: 939 AN: 4794

European-Finnish (FIN) AF: 0.0398 AC: 421 AN: 10568

Middle Eastern (MID) AF: 0.175 AC: 51 AN: 292

European-Non Finnish (NFE) AF: 0.0935 AC: 6350 AN: 67900

Other (OTH) AF: 0.190 AC: 401 AN: 2106

Alfa AF: 0.175 Hom.: 564

Bravo AF: 0.239

Asia WGS AF: 0.242 AC: 841 AN: 3478

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	2	not provided (2)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.5
DANN	Benign	0.49
PhyloP100		0.30
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs2915776; hg19: chr15-43922586;