rs7330752

Variant names:

• chr13-30282371-C-T
• rs7330752
• NM_032116.5:c.162+1245G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

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]

ENSG00000309792 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032116.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KATNAL1	NM_032116.5	MANE Select	c.162+1245G>A		intron	N/A	NP_115492.1	Q9BW62
	KATNAL1	NM_001014380.3		c.162+1245G>A		intron	N/A	NP_001014402.1	Q9BW62

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KATNAL1	ENST00000380615.8	TSL:1 MANE Select	c.162+1245G>A		intron	N/A	ENSP00000369989.3	Q9BW62
	KATNAL1	ENST00000908524.1		c.162+1245G>A		intron	N/A	ENSP00000578583.1
	KATNAL1	ENST00000908525.1		c.162+1245G>A		intron	N/A	ENSP00000578584.1

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

African (AFR) AF: 0.0642 AC: 2666 AN: 41540

American (AMR) AF: 0.0285 AC: 436 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0303 AC: 105 AN: 3466

East Asian (EAS) AF: 0.00 AC: 0 AN: 5184

South Asian (SAS) AF: 0.00891 AC: 43 AN: 4826

European-Finnish (FIN) AF: 0.00765 AC: 81 AN: 10594

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0357 AC: 2426 AN: 68012

Other (OTH) AF: 0.0398 AC: 84 AN: 2112

Alfa AF: 0.0371 Hom.: 158

Bravo AF: 0.0439

Asia WGS AF: 0.00664 AC: 23 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.74
DANN	Benign	0.30
PhyloP100		-1.1
Mutation Taster		=100/0	polymorphism

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

Other links and lift over

dbSNP: rs7330752; hg19: chr13-30856508;