rs648538

chr13-30238172-G-Achr13-30238172-G-T

Variant summary

Our verdict is Benign. Variant got -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

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]

LOC102723381 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KATNAL1	NM_032116.5	c.726+2288C>T		intron_variant		ENST00000380615.8
LOC102723381	XR_007063741.1	n.279+2472G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KATNAL1	ENST00000380615.8	c.726+2288C>T		intron_variant		1	NM_032116.5	P1
KATNAL1	ENST00000380617.7	c.726+2288C>T		intron_variant		2		P1

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

Gnomad4 AFR AF: 0.209

Gnomad4 AMR AF: 0.453

Gnomad4 ASJ AF: 0.370

Gnomad4 EAS AF: 0.351

Gnomad4 SAS AF: 0.340

Gnomad4 FIN AF: 0.462

Gnomad4 NFE AF: 0.328

Gnomad4 OTH AF: 0.328

Alfa AF: 0.331 Hom.: 17774

Bravo AF: 0.318

Asia WGS AF: 0.328 AC: 1139 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	2.3
Dann	Benign	0.75

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: rs648538; hg19: chr13-30812309;