2-218357123-G-A

Position:

• chr2-218357123-G-A

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The NM_198559.2(CATIP):​c.54G>A​(p.Ser18=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.203 in 1,612,536 control chromosomes in the GnomAD database, including 35,654 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 (2549 hom., cov: 30)
  • Exomes 𝑓: 0.21 (33105 hom.)
• Consequence: CATIP NM_198559.2 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.61

Genes affected

CATIP (HGNC:25062): (ciliogenesis associated TTC17 interacting protein) Involved in actin filament polymerization and cilium organization. Located in several cellular components, including actin cytoskeleton; nucleus; and plasma membrane. Implicated in spermatogenic failure. [provided by Alliance of Genome Resources, Apr 2022]

CATIP-AS2 (HGNC:41079): (CATIP antisense RNA 2)

ACMG classification

Verdict is Benign. Variant got -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BP7: Synonymous conserved (PhyloP=-1.61 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.25 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CATIP	NM_198559.2	c.54G>A	p.Ser18=	synonymous_variant	2/10	ENST00000289388.4	NP_940961.1
CATIP-AS2	NR_125777.1	n.53+791C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CATIP	ENST00000289388.4	c.54G>A	p.Ser18=	synonymous_variant	2/10	1	NM_198559.2	ENSP00000289388	P1
CATIP-AS2	ENST00000411433.1	n.53+791C>T		intron_variant, non_coding_transcript_variant		3
CATIP	ENST00000480532.1	n.76G>A		non_coding_transcript_exon_variant	2/2	3

Frequencies

GnomAD3 genomes AF: 0.167 AC: 25344 AN: 151846 Hom.: 2546 Cov.: 30

Gnomad AFR AF: 0.0625

Gnomad AMI AF: 0.268

Gnomad AMR AF: 0.256

Gnomad ASJ AF: 0.221

Gnomad EAS AF: 0.122

Gnomad SAS AF: 0.0674

Gnomad FIN AF: 0.152

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.217

Gnomad OTH AF: 0.210

GnomAD3 exomes AF: 0.187 AC: 46893 AN: 250848 Hom.: 5015 AF XY: 0.182 AC XY: 24725 AN XY: 135588

Gnomad AFR exome AF: 0.0608

Gnomad AMR exome AF: 0.284

Gnomad ASJ exome AF: 0.219

Gnomad EAS exome AF: 0.119

Gnomad SAS exome AF: 0.0658

Gnomad FIN exome AF: 0.164

Gnomad NFE exome AF: 0.219

Gnomad OTH exome AF: 0.226

GnomAD4 exome AF: 0.206 AC: 301238 AN: 1460572 Hom.: 33105 Cov.: 33 AF XY: 0.202 AC XY: 147046 AN XY: 726652

Gnomad4 AFR exome AF: 0.0547

Gnomad4 AMR exome AF: 0.284

Gnomad4 ASJ exome AF: 0.219

Gnomad4 EAS exome AF: 0.137

Gnomad4 SAS exome AF: 0.0671

Gnomad4 FIN exome AF: 0.163

Gnomad4 NFE exome AF: 0.223

Gnomad4 OTH exome AF: 0.199

GnomAD4 genome AF: 0.167 AC: 25357 AN: 151964 Hom.: 2549 Cov.: 30 AF XY: 0.165 AC XY: 12231 AN XY: 74260

Gnomad4 AFR AF: 0.0623

Gnomad4 AMR AF: 0.257

Gnomad4 ASJ AF: 0.221

Gnomad4 EAS AF: 0.122

Gnomad4 SAS AF: 0.0673

Gnomad4 FIN AF: 0.152

Gnomad4 NFE AF: 0.217

Gnomad4 OTH AF: 0.211

Alfa AF: 0.215 Hom.: 4754

Bravo AF: 0.176

Asia WGS AF: 0.0780 AC: 272 AN: 3478

EpiCase AF: 0.222

EpiControl AF: 0.228

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.2
DANN	Benign	0.56

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.060		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: rs4324314; hg19: chr2-219221846; COSMIC: COSV56822389; COSMIC: COSV56822389;