chr13-30232107-G-A

Variant names:

• chr13-30232107-G-A
• rs17505148
• NM_032116.5:c.727-635C>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.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
• 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]

ACMG classification

Our verdict: Benign. The variant received -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.

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.727-635C>T		intron	N/A	NP_115492.1
	KATNAL1	NM_001014380.3		c.727-635C>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.727-635C>T		intron	N/A	ENSP00000369989.3
	KATNAL1	ENST00000380617.7	TSL:2	c.727-635C>T		intron	N/A	ENSP00000369991.3

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

African (AFR) AF: 0.0846 AC: 3516 AN: 41536

American (AMR) AF: 0.109 AC: 1670 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.222 AC: 770 AN: 3470

East Asian (EAS) AF: 0.0686 AC: 356 AN: 5186

South Asian (SAS) AF: 0.0861 AC: 416 AN: 4830

European-Finnish (FIN) AF: 0.136 AC: 1440 AN: 10570

Middle Eastern (MID) AF: 0.195 AC: 57 AN: 292

European-Non Finnish (NFE) AF: 0.193 AC: 13110 AN: 67954

Other (OTH) AF: 0.166 AC: 350 AN: 2114

Alfa AF: 0.174 Hom.: 2219

Bravo AF: 0.139

Asia WGS AF: 0.112 AC: 389 AN: 3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	10
DANN	Benign	0.80
PhyloP100		-0.096
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: rs17505148; hg19: chr13-30806244;