rs2576036

chr18-47060731-A-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001387690.1(KATNAL2):c.549+1077A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.439 in 151,960 control chromosomes in the GnomAD database, including 14,769 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 0.44 (14769 hom., cov: 31)
• Consequence: KATNAL2 NM_001387690.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.627

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.534 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KATNAL2	NM_001387690.1	c.549+1077A>C		intron_variant		ENST00000683218.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KATNAL2	ENST00000683218.1	c.549+1077A>C		intron_variant			NM_001387690.1	P1

Frequencies

GnomAD3 genomes AF: 0.439 AC: 66723 AN: 151842 Hom.: 14763 Cov.: 31

Gnomad AFR AF: 0.369

Gnomad AMI AF: 0.324

Gnomad AMR AF: 0.543

Gnomad ASJ AF: 0.480

Gnomad EAS AF: 0.505

Gnomad SAS AF: 0.457

Gnomad FIN AF: 0.394

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.458

Gnomad OTH AF: 0.471

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.439 AC: 66756 AN: 151960 Hom.: 14769 Cov.: 31 AF XY: 0.440 AC XY: 32644 AN XY: 74266

Gnomad4 AFR AF: 0.369

Gnomad4 AMR AF: 0.543

Gnomad4 ASJ AF: 0.480

Gnomad4 EAS AF: 0.505

Gnomad4 SAS AF: 0.456

Gnomad4 FIN AF: 0.394

Gnomad4 NFE AF: 0.458

Gnomad4 OTH AF: 0.473

Alfa AF: 0.460 Hom.: 16715

Bravo AF: 0.447

Asia WGS AF: 0.507 AC: 1761 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	1.2
Dann	Benign	0.72

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: rs2576036; hg19: chr18-44587102;