14-91622511-A-G

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024764.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CATSPERB	NM_024764.4	MANE Select	c.1931-574T>C		intron	N/A	NP_079040.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CATSPERB	ENST00000256343.8	TSL:1 MANE Select	c.1931-574T>C		intron	N/A	ENSP00000256343.3
	CATSPERB	ENST00000557036.1	TSL:2	n.*412-574T>C		intron	N/A	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

African (AFR) AF: 0.636 AC: 26355 AN: 41464

American (AMR) AF: 0.819 AC: 12530 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.726 AC: 2518 AN: 3468

East Asian (EAS) AF: 0.972 AC: 5035 AN: 5178

South Asian (SAS) AF: 0.864 AC: 4170 AN: 4828

European-Finnish (FIN) AF: 0.829 AC: 8773 AN: 10578

Middle Eastern (MID) AF: 0.779 AC: 229 AN: 294

European-Non Finnish (NFE) AF: 0.749 AC: 50955 AN: 67998

Other (OTH) AF: 0.755 AC: 1597 AN: 2114

Alfa AF: 0.753 Hom.: 21327

Bravo AF: 0.736

Asia WGS AF: 0.891 AC: 3099 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	6.4
DANN	Benign	0.43
PhyloP100		-0.15
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1285635; hg19: chr14-92088855;