Genetic Variant KANSL1:c.*1520delA (chr17-46029955-CT-C) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The ENST00000262419.10(KANSL1):c.*1520delA variant causes a splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.15 in 145,282 control chromosomes in the GnomAD database, including 2,095 homozygotes. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.15 ( 2095 hom., cov: 28)

Exomes 𝑓: 0.092 ( 0 hom. )

Consequence

KANSL1
ENST00000262419.10 splice_region

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:2

Conservation

PhyloP100: 0.218

Publications

0 publications found

Variant links:

Genes affected

KANSL1 (HGNC:24565): (KAT8 regulatory NSL complex subunit 1) This gene encodes a nuclear protein that is a subunit of two protein complexes involved with histone acetylation, the MLL1 complex and the NSL1 complex. The encoded protein has been implicated in a variety of cellular processes including enhancer regulation, cell proliferation, and mitosis. Mutations in this gene are associated with Koolen-de Vries Syndrome. [provided by RefSeq, May 2022]

KANSL1 Gene-Disease associations (from GenCC):

Koolen-de Vries syndrome
Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: Ambry Genetics, G2P, Labcorp Genetics (formerly Invitae), ClinGen
Koolen-de Vries syndrome due to a point mutation
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

KANSL1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP6

Variant 17-46029955-CT-C is Benign according to our data. Variant chr17-46029955-CT-C is described in ClinVar as [Benign]. Clinvar id is 323732.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.22 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KANSL1	NM_015443.4 link	c.*1520delA		3_prime_UTR_variant	Exon 15 of 15	ENST00000432791.7	NP_056258.1	Q7Z3B3-1A0A024R9Y2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KANSL1	ENST00000432791.7 link	c.*1520delA		3_prime_UTR_variant	Exon 15 of 15	1	NM_015443.4	ENSP00000387393.3		Q7Z3B3-1

Frequencies

GnomAD3 genomes

AF:

0.150

AC:

21706

AN:

144930

Hom.:

2097

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0446

Gnomad AMI

AF:

0.281

Gnomad AMR

AF:

0.183

Gnomad ASJ

AF:

0.245

Gnomad EAS

AF:

0.00301

Gnomad SAS

AF:

0.0772

Gnomad FIN

AF:

0.0762

Gnomad MID

AF:

0.220

Gnomad NFE

AF:

0.223

Gnomad OTH

AF:

0.187

GnomAD4 exome

AF:

0.0915

AC:

AN:

306

Hom.:

Cov.:

AF XY:

0.0824

AC XY:

AN XY:

182

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.00

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.0940

AC:

AN:

298

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

Other (OTH)

AF:

0.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.527

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.150

AC:

21697

AN:

144976

Hom.:

2095

Cov.:

AF XY:

0.141

AC XY:

9933

AN XY:

70504

show subpopulations

African (AFR)

AF:

0.0446

AC:

1766

AN:

39624

American (AMR)

AF:

0.183

AC:

2636

AN:

14428

Ashkenazi Jewish (ASJ)

AF:

0.245

AC:

833

AN:

3398

East Asian (EAS)

AF:

0.00322

AC:

AN:

4972

South Asian (SAS)

AF:

0.0775

AC:

352

AN:

4542

European-Finnish (FIN)

AF:

0.0762

AC:

675

AN:

8858

Middle Eastern (MID)

AF:

0.219

AC:

AN:

278

European-Non Finnish (NFE)

AF:

0.223

AC:

14738

AN:

65986

Other (OTH)

AF:

0.185

AC:

369

AN:

1996

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.491

Heterozygous variant carriers

799

1599

2398

3198

3997

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.0326

Hom.:

Bravo

AF:

0.148

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

Syndromic intellectual disability

Benign:1

Jun 14, 2016

Illumina Laboratory Services, Illumina

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

MAPT-Related Spectrum Disorders

Benign:1

Jun 14, 2016

Illumina Laboratory Services, Illumina

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.22

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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17-46029955-CT-C

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over