19-38368403-T-C

Position:

• chr19-38368403-T-C

Variant summary

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

The NM_021185.5(CATSPERG):​c.3020+266T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.17 in 152,208 control chromosomes in the GnomAD database, including 2,948 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 (2948 hom., cov: 32)
• Consequence: CATSPERG NM_021185.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.201

Genes affected

CATSPERG (HGNC:25243): (cation channel sperm associated auxiliary subunit gamma) CATSPERG is a subunit of the CATSPER (see CATSPER1; MIM 606389) sperm calcium channel, which is required for sperm hyperactivated motility and male fertility (Wang et al., 2009 [PubMed 19516020]).[supplied by OMIM, Jul 2010]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.52 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CATSPERG	NM_021185.5	c.3020+266T>C		intron_variant		ENST00000409235.8	NP_067008.3
CATSPERG	NM_001330496.2	c.2900+266T>C		intron_variant			NP_001317425.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CATSPERG	ENST00000409235.8	c.3020+266T>C		intron_variant		5	NM_021185.5	ENSP00000386962	P1

Frequencies

GnomAD3 genomes AF: 0.170 AC: 25828 AN: 152090 Hom.: 2945 Cov.: 32

Gnomad AFR AF: 0.228

Gnomad AMI AF: 0.0471

Gnomad AMR AF: 0.237

Gnomad ASJ AF: 0.131

Gnomad EAS AF: 0.539

Gnomad SAS AF: 0.228

Gnomad FIN AF: 0.106

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.101

Gnomad OTH AF: 0.161

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

GnomAD4 genome AF: 0.170 AC: 25882 AN: 152208 Hom.: 2948 Cov.: 32 AF XY: 0.176 AC XY: 13086 AN XY: 74430

Gnomad4 AFR AF: 0.229

Gnomad4 AMR AF: 0.236

Gnomad4 ASJ AF: 0.131

Gnomad4 EAS AF: 0.537

Gnomad4 SAS AF: 0.229

Gnomad4 FIN AF: 0.106

Gnomad4 NFE AF: 0.101

Gnomad4 OTH AF: 0.163

Alfa AF: 0.122 Hom.: 2512

Bravo AF: 0.183

Asia WGS AF: 0.368 AC: 1276 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	4.2
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: rs11880532; hg19: chr19-38859043;