rs17505148

chr13-30232107-G-A

Variant summary

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

The NM_032116.5(KATNAL1):c.727-635C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.143 in 152,128 control chromosomes in the GnomAD database, including 1,786 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 (1786 hom., cov: 33)
• Consequence: KATNAL1 NM_032116.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0960

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=-0.76).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.19 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KATNAL1	NM_032116.5	c.727-635C>T		intron_variant		ENST00000380615.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KATNAL1	ENST00000380615.8	c.727-635C>T		intron_variant		1	NM_032116.5	P1
KATNAL1	ENST00000380617.7	c.727-635C>T		intron_variant		2		P1

Frequencies

GnomAD3 genomes AF: 0.143 AC: 21767 AN: 152010 Hom.: 1778 Cov.: 33

Gnomad AFR AF: 0.0845

Gnomad AMI AF: 0.114

Gnomad AMR AF: 0.110

Gnomad ASJ AF: 0.222

Gnomad EAS AF: 0.0681

Gnomad SAS AF: 0.0863

Gnomad FIN AF: 0.136

Gnomad MID AF: 0.191

Gnomad NFE AF: 0.193

Gnomad OTH AF: 0.159

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

GnomAD4 genome AF: 0.143 AC: 21789 AN: 152128 Hom.: 1786 Cov.: 33 AF XY: 0.139 AC XY: 10321 AN XY: 74360

Gnomad4 AFR AF: 0.0846

Gnomad4 AMR AF: 0.109

Gnomad4 ASJ AF: 0.222

Gnomad4 EAS AF: 0.0686

Gnomad4 SAS AF: 0.0861

Gnomad4 FIN AF: 0.136

Gnomad4 NFE AF: 0.193

Gnomad4 OTH AF: 0.166

Alfa AF: 0.166 Hom.: 1282

Bravo AF: 0.139

Asia WGS AF: 0.112 AC: 389 AN: 3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
Cadd	Benign	10
Dann	Benign	0.80

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: rs17505148; hg19: chr13-30806244;