18-46969679-C-T

Variant names:

• chr18-46969679-C-T
• rs1465498237
• NM_001387690.1:c.51+22756C>T

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_Strong BP6_Moderate

The NM_001387690.1(KATNAL2):​c.51+22756C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.0019 (0 hom., cov: 20)
  • Exomes 𝑓: 0.00060 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: KATNAL2 NM_001387690.1 intron
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -4.25

Genes affected

KATNAL2 (HGNC:25387): (katanin catalytic subunit A1 like 2) Predicted to enable microtubule-severing ATPase activity. Predicted to be involved in cytoplasmic microtubule organization. Located in cytoplasm; microtubule; and spindle pole. [provided by Alliance of Genome Resources, Apr 2022]

ELOA3CP (HGNC:52410): (elongin A3 family member C, pseudogene) Predicted to be involved in transcription elongation from RNA polymerase II promoter. Predicted to be part of elongin complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Likely_benign. Variant got -6 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BP6: Variant 18-46969679-C-T is Benign according to our data. Variant chr18-46969679-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 3770930.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KATNAL2	NM_001387690.1	c.51+22756C>T		intron_variant	Intron 3 of 17	ENST00000683218.1	NP_001374619.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KATNAL2	ENST00000683218.1	c.51+22756C>T		intron_variant	Intron 3 of 17		NM_001387690.1	ENSP00000508137.1

Frequencies

GnomAD3 genomes AF: 0.00 AC: 190 AN: 102374 Hom.: 0 Cov.: 20 FAILED QC

Gnomad AFR AF: 0.000464

Gnomad AMI AF: 0.0112

Gnomad AMR AF: 0.00171

Gnomad ASJ AF: 0.00275

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00257

Gnomad FIN AF: 0.00157

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00279

Gnomad OTH AF: 0.000717

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.000602 AC: 217 AN: 360398 Hom.: 0 Cov.: 0 AF XY: 0.000586 AC XY: 111 AN XY: 189486

Gnomad4 AFR exome AF: 0.000207

Gnomad4 AMR exome AF: 0.000239

Gnomad4 ASJ exome AF: 0.000101

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000218

Gnomad4 FIN exome AF: 0.000303

Gnomad4 NFE exome AF: 0.000848

Gnomad4 OTH exome AF: 0.000585

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00185 AC: 190 AN: 102446 Hom.: 0 Cov.: 20 AF XY: 0.00184 AC XY: 91 AN XY: 49356

Gnomad4 AFR AF: 0.000463

Gnomad4 AMR AF: 0.00170

Gnomad4 ASJ AF: 0.00275

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00258

Gnomad4 FIN AF: 0.00157

Gnomad4 NFE AF: 0.00279

Gnomad4 OTH AF: 0.000708

Alfa AF: 0.000674 Hom.: 0

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Feb 01, 2025

CeGaT Center for Human Genetics Tuebingen

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

ELOA3BP: PM2:Supporting, BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	9.7

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1465498237; hg19: chr18-44549642;