18-46969049-T-C

Position:

• chr18-46969049-T-C

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+22126T>C 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 0.0031 (4 hom., cov: 17)
  • Exomes 𝑓: 0.00033 (9 hom.)
  • Failed GnomAD Quality Control
• Consequence: KATNAL2 NM_001387690.1 intron
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.856

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:):

ACMG classification

Verdict is Likely_benign. Variant got -6 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BP6: Variant 18-46969049-T-C is Benign according to our data. Variant chr18-46969049-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 3388358.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KATNAL2	NM_001387690.1	c.51+22126T>C		intron_variant		ENST00000683218.1	NP_001374619.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KATNAL2	ENST00000683218.1	c.51+22126T>C		intron_variant			NM_001387690.1	ENSP00000508137.1

Frequencies

GnomAD3 genomes AF: 0.00 AC: 306 AN: 99670 Hom.: 4 Cov.: 17 FAILED QC

Gnomad AFR AF: 0.0111

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000621

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000451

Gnomad OTH AF: 0.00227

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.000332 AC: 336 AN: 1012878 Hom.: 9 Cov.: 26 AF XY: 0.000275 AC XY: 139 AN XY: 505020

Gnomad4 AFR exome AF: 0.0126

Gnomad4 AMR exome AF: 0.000532

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000151

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0000119

Gnomad4 OTH exome AF: 0.000709

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00306 AC: 305 AN: 99766 Hom.: 4 Cov.: 17 AF XY: 0.00297 AC XY: 145 AN XY: 48854

Gnomad4 AFR AF: 0.0110

Gnomad4 AMR AF: 0.000620

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000451

Gnomad4 OTH AF: 0.00224

Alfa AF: 0.0188 Hom.: 5

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Nov 01, 2024

ELOA3BP: BP4, BP7, BS1 -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	6.1
DANN	Benign	0.50

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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: rs201366170; hg19: chr18-44549012;