Genetic Variant KATNAL1:c.163-102C>A (chr13-30280325-G-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_032116.5(KATNAL1):c.163-102C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.623 in 776,234 control chromosomes in the GnomAD database, including 152,746 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 0.66 ( 33198 hom., cov: 32)

Exomes 𝑓: 0.62 ( 119548 hom. )

Consequence

KATNAL1
NM_032116.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.887

Publications

3 publications found

Variant links:

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]

KATNAL1 links:

ENSG00000309792 (HGNC:):

ENSG00000309792 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.93).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.75 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KATNAL1	NM_032116.5	MANE Select	c.163-102C>A		intron	N/A	NP_115492.1	Q9BW62
	KATNAL1	NM_001014380.3		c.163-102C>A		intron	N/A	NP_001014402.1	Q9BW62

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
KATNAL1	ENST00000380615.8	TSL:1 MANE Select	c.163-102C>A	intron	N/A	ENSP00000369989.3	Q9BW62
KATNAL1	ENST00000908524.1		c.163-102C>A	intron	N/A	ENSP00000578583.1
KATNAL1	ENST00000908525.1		c.163-102C>A	intron	N/A	ENSP00000578584.1

Frequencies

GnomAD3 genomes

AF:

0.655

AC:

99510

AN:

151828

Hom.:

33158

Cov.:

show subpopulations

Gnomad AFR

AF:

0.757

Gnomad AMI

AF:

0.498

Gnomad AMR

AF:

0.693

Gnomad ASJ

AF:

0.615

Gnomad EAS

AF:

0.717

Gnomad SAS

AF:

0.589

Gnomad FIN

AF:

0.515

Gnomad MID

AF:

0.650

Gnomad NFE

AF:

0.611

Gnomad OTH

AF:

0.669

GnomAD4 exome

AF:

0.615

AC:

384021

AN:

624292

Hom.:

119548

AF XY:

0.615

AC XY:

192540

AN XY:

313014

show subpopulations

African (AFR)

AF:

0.757

AC:

10464

AN:

13828

American (AMR)

AF:

0.737

AC:

9204

AN:

12496

Ashkenazi Jewish (ASJ)

AF:

0.606

AC:

8057

AN:

13296

East Asian (EAS)

AF:

0.726

AC:

20009

AN:

27542

South Asian (SAS)

AF:

0.593

AC:

14575

AN:

24596

European-Finnish (FIN)

AF:

0.531

AC:

15549

AN:

29262

Middle Eastern (MID)

AF:

0.654

AC:

1411

AN:

2158

European-Non Finnish (NFE)

AF:

0.607

AC:

286068

AN:

471112

Other (OTH)

AF:

0.623

AC:

18684

AN:

30002

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.508

Heterozygous variant carriers

7022

14044

21067

28089

35111

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

6352

12704

19056

25408

31760

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.655

AC:

99598

AN:

151942

Hom.:

33198

Cov.:

AF XY:

0.654

AC XY:

48565

AN XY:

74256

show subpopulations

African (AFR)

AF:

0.757

AC:

31378

AN:

41456

American (AMR)

AF:

0.693

AC:

10587

AN:

15270

Ashkenazi Jewish (ASJ)

AF:

0.615

AC:

2131

AN:

3466

East Asian (EAS)

AF:

0.717

AC:

3713

AN:

5180

South Asian (SAS)

AF:

0.587

AC:

2829

AN:

4818

European-Finnish (FIN)

AF:

0.515

AC:

5392

AN:

10474

Middle Eastern (MID)

AF:

0.661

AC:

193

AN:

292

European-Non Finnish (NFE)

AF:

0.611

AC:

41507

AN:

67966

Other (OTH)

AF:

0.670

AC:

1416

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

1737

3473

5210

6946

8683

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

796

1592

2388

3184

3980

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.635

Hom.:

66611

Bravo

AF:

0.677

Asia WGS

AF:

0.655

AC:

2271

AN:

3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

0.21

(source)

DANN

Benign

0.41

PhyloP100

-0.89

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over