Variant 17-46033166-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1

The NM_015443.4(KANSL1):c.2751C>T(p.Phe917=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.188 in 1,600,854 control chromosomes in the GnomAD database, including 32,471 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.14 ( 2102 hom., cov: 32)

Exomes 𝑓: 0.19 ( 30369 hom. )

Consequence

KANSL1
NM_015443.4 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:6

Conservation

PhyloP100: 0.0610

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 -19 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.46).

BP6

Variant 17-46033166-G-A is Benign according to our data. Variant chr17-46033166-G-A is described in ClinVar as [Benign]. Clinvar id is 323765.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-46033166-G-A is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=0.061 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.214 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KANSL1	NM_015443.4 linkuse as main transcript	c.2751C>T	p.Phe917=	synonymous_variant	13/15	ENST00000432791.7	NP_056258.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KANSL1	ENST00000432791.7 linkuse as main transcript	c.2751C>T	p.Phe917=	synonymous_variant	13/15	1	NM_015443.4	ENSP00000387393	P4

Frequencies

GnomAD3 genomes

AF:

0.143

AC:

21742

AN:

152008

Hom.:

2103

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0428

Gnomad AMI

AF:

0.274

Gnomad AMR

AF:

0.176

Gnomad ASJ

AF:

0.240

Gnomad EAS

AF:

0.00154

Gnomad SAS

AF:

0.0738

Gnomad FIN

AF:

0.0649

Gnomad MID

AF:

0.215

Gnomad NFE

AF:

0.217

Gnomad OTH

AF:

0.180

GnomAD3 exomes

AF:

0.143

AC:

33062

AN:

231482

Hom.:

3076

AF XY:

0.146

AC XY:

18214

AN XY:

124628

show subpopulations

Gnomad AFR exome

AF:

0.0384

Gnomad AMR exome

AF:

0.117

Gnomad ASJ exome

AF:

0.254

Gnomad EAS exome

AF:

0.000623

Gnomad SAS exome

AF:

0.0746

Gnomad FIN exome

AF:

0.0664

Gnomad NFE exome

AF:

0.211

Gnomad OTH exome

AF:

0.176

GnomAD4 exome

AF:

0.193

AC:

279548

AN:

1448726

Hom.:

30369

Cov.:

AF XY:

0.190

AC XY:

137063

AN XY:

719498

show subpopulations

Gnomad4 AFR exome

AF:

0.0363

Gnomad4 AMR exome

AF:

0.124

Gnomad4 ASJ exome

AF:

0.256

Gnomad4 EAS exome

AF:

0.000889

Gnomad4 SAS exome

AF:

0.0789

Gnomad4 FIN exome

AF:

0.0719

Gnomad4 NFE exome

AF:

0.221

Gnomad4 OTH exome

AF:

0.177

GnomAD4 genome

AF:

0.143

AC:

21733

AN:

152128

Hom.:

2102

Cov.:

AF XY:

0.134

AC XY:

9950

AN XY:

74390

show subpopulations

Gnomad4 AFR

AF:

0.0427

Gnomad4 AMR

AF:

0.175

Gnomad4 ASJ

AF:

0.240

Gnomad4 EAS

AF:

0.00155

Gnomad4 SAS

AF:

0.0739

Gnomad4 FIN

AF:

0.0649

Gnomad4 NFE

AF:

0.217

Gnomad4 OTH

AF:

0.178

Alfa

AF:

0.195

Hom.:

2515

Bravo

AF:

0.148

Asia WGS

AF:

0.0310

AC:

109

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:6

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Benign, criteria provided, single submitter	clinical testing	GeneDx	Mar 03, 2015	- -
Benign, criteria provided, single submitter	clinical testing	Athena Diagnostics	Apr 20, 2017	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Syndromic intellectual disability

Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

MAPT-Related Spectrum Disorders

Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Koolen-de Vries syndrome

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Feb 01, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.46

CADD

Benign

1.1

DANN

Benign

0.87

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