rs7330752

chr13-30282371-C-T

Variant summary

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

The NM_032116.5(KATNAL1):c.162+1245G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0394 in 152,244 control chromosomes in the GnomAD database, including 163 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 0.039 (163 hom., cov: 31)
• Consequence: KATNAL1 NM_032116.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13

Genes affected

KATNAL1 (HGNC:28361): (katanin catalytic subunit A1 like 1) Enables identical protein binding activity and microtubule-severing ATPase activity. Involved in microtubule severing. 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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0621 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KATNAL1	NM_032116.5	c.162+1245G>A		intron_variant		ENST00000380615.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KATNAL1	ENST00000380615.8	c.162+1245G>A		intron_variant		1	NM_032116.5	P1
KATNAL1	ENST00000380617.7	c.162+1245G>A		intron_variant		2		P1
KATNAL1	ENST00000414289.5	c.162+1245G>A		intron_variant		4
KATNAL1	ENST00000441394.1	c.162+1245G>A		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.0394 AC: 5994 AN: 152126 Hom.: 162 Cov.: 31

Gnomad AFR AF: 0.0640

Gnomad AMI AF: 0.170

Gnomad AMR AF: 0.0286

Gnomad ASJ AF: 0.0303

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00890

Gnomad FIN AF: 0.00765

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0357

Gnomad OTH AF: 0.0402

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

GnomAD4 genome AF: 0.0394 AC: 6006 AN: 152244 Hom.: 163 Cov.: 31 AF XY: 0.0362 AC XY: 2693 AN XY: 74440

Gnomad4 AFR AF: 0.0642

Gnomad4 AMR AF: 0.0285

Gnomad4 ASJ AF: 0.0303

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00891

Gnomad4 FIN AF: 0.00765

Gnomad4 NFE AF: 0.0357

Gnomad4 OTH AF: 0.0398

Alfa AF: 0.0371 Hom.: 141

Bravo AF: 0.0439

Asia WGS AF: 0.00664 AC: 23 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.74
Dann	Benign	0.30

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: rs7330752; hg19: chr13-30856508;