Variant 17-46031438-CAATA-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBS1BS2

The NM_015443.4(KANSL1):c.*34_*37delTATT variant causes a 3 prime UTR change. The variant allele was found at a frequency of 0.00296 in 1,526,256 control chromosomes in the GnomAD database, including 53 homozygotes. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.0029 ( 3 hom., cov: 32)

Exomes 𝑓: 0.0030 ( 50 hom. )

Consequence

KANSL1
NM_015443.4 3_prime_UTR

Scores

Not classified

Clinical Significance

Likely benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 3.64

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 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP6

Variant 17-46031438-CAATA-C is Benign according to our data. Variant chr17-46031438-CAATA-C is described in ClinVar as [Likely_benign]. Clinvar id is 323760.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS1

Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.00292 (445/152272) while in subpopulation EAS AF= 0.0178 (92/5182). AF 95% confidence interval is 0.0148. There are 3 homozygotes in gnomad4. There are 263 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High AC in GnomAd4 at 445 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KANSL1	NM_015443.4 link	c.34_37delTATT		3_prime_UTR_variant	15/15	ENST00000432791.7	NP_056258.1	Q7Z3B3-1A0A024R9Y2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KANSL1	ENST00000432791 link	c.34_37delTATT		3_prime_UTR_variant	15/15	1	NM_015443.4	ENSP00000387393.3		Q7Z3B3-1

Frequencies

GnomAD3 genomes

AF:

0.00292

AC:

445

AN:

152154

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000483

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000523

Gnomad ASJ

AF:

0.00894

Gnomad EAS

AF:

0.0177

Gnomad SAS

AF:

0.00579

Gnomad FIN

AF:

0.0162

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00160

Gnomad OTH

AF:

0.00144

GnomAD3 exomes

AF:

0.00469

AC:

851

AN:

181600

Hom.:

AF XY:

0.00480

AC XY:

466

AN XY:

96996

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.0000386

Gnomad ASJ exome

AF:

0.00656

Gnomad EAS exome

AF:

0.0166

Gnomad SAS exome

AF:

0.00529

Gnomad FIN exome

AF:

0.0180

Gnomad NFE exome

AF:

0.00148

Gnomad OTH exome

AF:

0.00343

GnomAD4 exome

AF:

0.00296

AC:

4067

AN:

1373984

Hom.:

AF XY:

0.00304

AC XY:

2047

AN XY:

673908

show subpopulations

Gnomad4 AFR exome

AF:

0.000125

Gnomad4 AMR exome

AF:

0.000111

Gnomad4 ASJ exome

AF:

0.00573

Gnomad4 EAS exome

AF:

0.0349

Gnomad4 SAS exome

AF:

0.00568

Gnomad4 FIN exome

AF:

0.0150

Gnomad4 NFE exome

AF:

0.00119

Gnomad4 OTH exome

AF:

0.00261

GnomAD4 genome

AF:

0.00292

AC:

445

AN:

152272

Hom.:

Cov.:

AF XY:

0.00353

AC XY:

263

AN XY:

74454

show subpopulations

Gnomad4 AFR

AF:

0.0000481

Gnomad4 AMR

AF:

0.000523

Gnomad4 ASJ

AF:

0.00894

Gnomad4 EAS

AF:

0.0178

Gnomad4 SAS

AF:

0.00580

Gnomad4 FIN

AF:

0.0162

Gnomad4 NFE

AF:

0.00160

Gnomad4 OTH

AF:

0.00142

Alfa

AF:

0.00251

Hom.:

Bravo

AF:

0.00151

Asia WGS

AF:

0.00953

AC:

AN:

3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Syndromic intellectual disability

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

MAPT-Related Spectrum Disorders

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

GeneDx

Jul 17, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over