13-30238172-G-A

Variant names:

• chr13-30238172-G-A
• rs648538
• NM_032116.5:c.726+2288C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_032116.5(KATNAL1):​c.726+2288C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.32 in 151,910 control chromosomes in the GnomAD database, including 8,283 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 0.32 (8283 hom., cov: 32)
• Consequence: KATNAL1 NM_032116.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.209
• Publications: 4 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.444 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KATNAL1	NM_032116.5	MANE Select	c.726+2288C>T		intron	N/A	NP_115492.1
	KATNAL1	NM_001014380.3		c.726+2288C>T		intron	N/A	NP_001014402.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KATNAL1	ENST00000380615.8	TSL:1 MANE Select	c.726+2288C>T		intron	N/A	ENSP00000369989.3
	KATNAL1	ENST00000380617.7	TSL:2	c.726+2288C>T		intron	N/A	ENSP00000369991.3
	ENSG00000309792	ENST00000843926.1		n.218+2472G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.320 AC: 48571 AN: 151792 Hom.: 8278 Cov.: 32

Gnomad AFR AF: 0.209

Gnomad AMI AF: 0.371

Gnomad AMR AF: 0.452

Gnomad ASJ AF: 0.370

Gnomad EAS AF: 0.352

Gnomad SAS AF: 0.340

Gnomad FIN AF: 0.462

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.328

Gnomad OTH AF: 0.330

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

GnomAD4 genome AF: 0.320 AC: 48589 AN: 151910 Hom.: 8283 Cov.: 32 AF XY: 0.327 AC XY: 24298 AN XY: 74232

African (AFR) AF: 0.209 AC: 8661 AN: 41448

American (AMR) AF: 0.453 AC: 6908 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.370 AC: 1285 AN: 3472

East Asian (EAS) AF: 0.351 AC: 1812 AN: 5158

South Asian (SAS) AF: 0.340 AC: 1638 AN: 4814

European-Finnish (FIN) AF: 0.462 AC: 4863 AN: 10522

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.328 AC: 22297 AN: 67926

Other (OTH) AF: 0.328 AC: 691 AN: 2106

Alfa AF: 0.326 Hom.: 27160

Bravo AF: 0.318

Asia WGS AF: 0.328 AC: 1139 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.3
DANN	Benign	0.75
PhyloP100		0.21
Mutation Taster		=100/0	polymorphism (auto)

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: rs648538; hg19: chr13-30812309;