rs17724817

Variant names:

• chr13-30234771-A-G
• rs17724817
• NM_032116.5:c.727-3299T>C

Variant summary

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

The NM_032116.5(KATNAL1):​c.727-3299T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.144 in 152,172 control chromosomes in the GnomAD database, including 1,811 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 0.14 (1811 hom., cov: 32)
• Consequence: KATNAL1 NM_032116.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.351
• Publications: 0 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=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.191 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.727-3299T>C		intron	N/A	NP_115492.1
	KATNAL1	NM_001014380.3		c.727-3299T>C		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.727-3299T>C		intron	N/A	ENSP00000369989.3
	KATNAL1	ENST00000380617.7	TSL:2	c.727-3299T>C		intron	N/A	ENSP00000369991.3
	ENSG00000309792	ENST00000843926.1		n.-194A>G		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.144 AC: 21883 AN: 152054 Hom.: 1803 Cov.: 32

Gnomad AFR AF: 0.0855

Gnomad AMI AF: 0.114

Gnomad AMR AF: 0.111

Gnomad ASJ AF: 0.221

Gnomad EAS AF: 0.0685

Gnomad SAS AF: 0.0870

Gnomad FIN AF: 0.136

Gnomad MID AF: 0.188

Gnomad NFE AF: 0.194

Gnomad OTH AF: 0.159

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

GnomAD4 genome AF: 0.144 AC: 21905 AN: 152172 Hom.: 1811 Cov.: 32 AF XY: 0.140 AC XY: 10396 AN XY: 74422

African (AFR) AF: 0.0856 AC: 3553 AN: 41516

American (AMR) AF: 0.111 AC: 1693 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.221 AC: 767 AN: 3468

East Asian (EAS) AF: 0.0690 AC: 358 AN: 5188

South Asian (SAS) AF: 0.0869 AC: 419 AN: 4824

European-Finnish (FIN) AF: 0.136 AC: 1443 AN: 10582

Middle Eastern (MID) AF: 0.192 AC: 56 AN: 292

European-Non Finnish (NFE) AF: 0.194 AC: 13161 AN: 67982

Other (OTH) AF: 0.166 AC: 351 AN: 2114

Alfa AF: 0.172 Hom.: 2338

Bravo AF: 0.140

Asia WGS AF: 0.113 AC: 395 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.9
DANN	Benign	0.85
PhyloP100		-0.35
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: rs17724817; hg19: chr13-30808908;