chr1-244605783-ACTATGG-A

Position:

• chr1-244605783-ACTATGG-A

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM4 BS2

The NM_001130957.2(CATSPERE):​c.2394_2399del​(p.Met799_Ala800del) variant causes a inframe deletion change. The variant allele was found at a frequency of 0.00194 in 1,609,554 control chromosomes in the GnomAD database, including 5 homozygotes. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency:
  • Genomes: 𝑓 0.0014 (1 hom., cov: 31)
  • Exomes 𝑓: 0.0020 (4 hom.)
• Consequence: CATSPERE NM_001130957.2 inframe_deletion
• Clinical Significance: Uncertain significance criteria provided, single submitter U:2
• Conservation: PhyloP100: 4.84

Genes affected

CATSPERE (HGNC:28491): (catsper channel auxiliary subunit epsilon) Located in sperm principal piece. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM4: Nonframeshift variant in NON repetitive region in NM_001130957.2.
• BS2: High Homozygotes in GnomAdExome4 at 4 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CATSPERE	NM_001130957.2	c.2394_2399del	p.Met799_Ala800del	inframe_deletion	18/22	ENST00000366534.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CATSPERE	ENST00000366534.9	c.2394_2399del	p.Met799_Ala800del	inframe_deletion	18/22	2	NM_001130957.2	P2

Frequencies

GnomAD3 genomes AF: 0.00136 AC: 207 AN: 152230 Hom.: 1 Cov.: 31

Gnomad AFR AF: 0.000579

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00164

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00124

Gnomad FIN AF: 0.000377

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00213

Gnomad OTH AF: 0.00143

GnomAD3 exomes AF: 0.00117 AC: 293 AN: 249996 Hom.: 0 AF XY: 0.00124 AC XY: 167 AN XY: 135080

Gnomad AFR exome AF: 0.000370

Gnomad AMR exome AF: 0.000789

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.000764

Gnomad FIN exome AF: 0.000647

Gnomad NFE exome AF: 0.00194

Gnomad OTH exome AF: 0.000492

GnomAD4 exome AF: 0.00200 AC: 2916 AN: 1457206 Hom.: 4 AF XY: 0.00190 AC XY: 1377 AN XY: 725164

Gnomad4 AFR exome AF: 0.000269

Gnomad4 AMR exome AF: 0.000697

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000804

Gnomad4 FIN exome AF: 0.000562

Gnomad4 NFE exome AF: 0.00245

Gnomad4 OTH exome AF: 0.00105

GnomAD4 genome AF: 0.00136 AC: 207 AN: 152348 Hom.: 1 Cov.: 31 AF XY: 0.00133 AC XY: 99 AN XY: 74502

Gnomad4 AFR AF: 0.000577

Gnomad4 AMR AF: 0.00163

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00124

Gnomad4 FIN AF: 0.000377

Gnomad4 NFE AF: 0.00213

Gnomad4 OTH AF: 0.00142

Alfa AF: 0.000409 Hom.: 0

Bravo AF: 0.00130

EpiCase AF: 0.00252

EpiControl AF: 0.00196

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:2

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Uncertain:2

Uncertain significance, no assertion criteria provided	literature only	OMIM	Jul 24, 2019	- -
Uncertain significance, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Nov 01, 2021	- -

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs761237686; hg19: chr1-244769085;