13-30234771-A-G

Position:

• chr13-30234771-A-G

Variant summary

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

The ENST00000380615.8(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 ENST00000380615.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.351

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=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.191 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KATNAL1	NM_032116.5	c.727-3299T>C		intron_variant		ENST00000380615.8	NP_115492.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KATNAL1	ENST00000380615.8	c.727-3299T>C		intron_variant		1	NM_032116.5	ENSP00000369989	P1
KATNAL1	ENST00000380617.7	c.727-3299T>C		intron_variant		2		ENSP00000369991	P1

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

Gnomad4 AFR AF: 0.0856

Gnomad4 AMR AF: 0.111

Gnomad4 ASJ AF: 0.221

Gnomad4 EAS AF: 0.0690

Gnomad4 SAS AF: 0.0869

Gnomad4 FIN AF: 0.136

Gnomad4 NFE AF: 0.194

Gnomad4 OTH AF: 0.166

Alfa AF: 0.175 Hom.: 1682

Bravo AF: 0.140

Asia WGS AF: 0.113 AC: 395 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.9
DANN	Benign	0.85

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: rs17724817; hg19: chr13-30808908;