GeneBe

rs648538

Positions:

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.209
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]

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ACMG classification

Classification made for transcript

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
KATNAL1NM_032116.5 linkuse as main transcriptc.726+2288C>T intron_variant ENST00000380615.8
LOC102723381XR_007063741.1 linkuse as main transcriptn.279+2472G>A intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
KATNAL1ENST00000380615.8 linkuse as main transcriptc.726+2288C>T intron_variant 1 NM_032116.5 P1
KATNAL1ENST00000380617.7 linkuse as main transcriptc.726+2288C>T intron_variant 2 P1

Frequencies

GnomAD3 genomes
AF:
0.320
AC:
48571
AN:
151792
Hom.:
8278
Cov.:
32
show subpopulations
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
show subpopulations
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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs648538; hg19: chr13-30812309; API