14-91622511-A-G

Variant names:

• chr14-91622511-A-G
• rs1285635
• NM_024764.4:c.1931-574T>C

Variant summary

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

The NM_024764.4(CATSPERB):​c.1931-574T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.742 in 152,118 control chromosomes in the GnomAD database, including 42,414 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 0.74 (42414 hom., cov: 31)
• Consequence: CATSPERB NM_024764.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.149

Genes affected

CATSPERB (HGNC:20500): (cation channel sperm associated auxiliary subunit beta) Predicted to be involved in cell differentiation and spermatogenesis. Predicted to be located in plasma membrane. Predicted to be part of CatSper complex. Predicted to be active in cilium. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.95 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CATSPERB	NM_024764.4	c.1931-574T>C		intron_variant	Intron 18 of 26	ENST00000256343.8	NP_079040.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CATSPERB	ENST00000256343.8	c.1931-574T>C		intron_variant	Intron 18 of 26	1	NM_024764.4	ENSP00000256343.3
CATSPERB	ENST00000557036.1	n.*412-574T>C		intron_variant	Intron 4 of 12	2		ENSP00000451083.1

Frequencies

GnomAD3 genomes AF: 0.742 AC: 112753 AN: 152000 Hom.: 42395 Cov.: 31

Gnomad AFR AF: 0.636

Gnomad AMI AF: 0.726

Gnomad AMR AF: 0.819

Gnomad ASJ AF: 0.726

Gnomad EAS AF: 0.973

Gnomad SAS AF: 0.865

Gnomad FIN AF: 0.829

Gnomad MID AF: 0.782

Gnomad NFE AF: 0.749

Gnomad OTH AF: 0.760

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

GnomAD4 genome AF: 0.742 AC: 112818 AN: 152118 Hom.: 42414 Cov.: 31 AF XY: 0.751 AC XY: 55841 AN XY: 74346

Gnomad4 AFR AF: 0.636

Gnomad4 AMR AF: 0.819

Gnomad4 ASJ AF: 0.726

Gnomad4 EAS AF: 0.972

Gnomad4 SAS AF: 0.864

Gnomad4 FIN AF: 0.829

Gnomad4 NFE AF: 0.749

Gnomad4 OTH AF: 0.755

Alfa AF: 0.754 Hom.: 19155

Bravo AF: 0.736

Asia WGS AF: 0.891 AC: 3099 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	6.4
DANN	Benign	0.43

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.070		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: rs1285635; hg19: chr14-92088855;