Genetic Variant KANSL3:c.2616+87A>G (chr2-96601556-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_001115016.3(KANSL3):c.2616+87A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.284 in 1,518,732 control chromosomes in the GnomAD database, including 72,117 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 0.24 ( 6002 hom., cov: 32)

Exomes 𝑓: 0.29 ( 66115 hom. )

Consequence

KANSL3
NM_001115016.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.36

Publications

8 publications found

Variant links:

Genes affected

KANSL3 (HGNC:25473): (KAT8 regulatory NSL complex subunit 3) Involved in histone H4-K16 acetylation; histone H4-K5 acetylation; and histone H4-K8 acetylation. Located in nucleoplasm. Part of histone acetyltransferase complex. [provided by Alliance of Genome Resources, Apr 2022]

KANSL3 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=-0.89).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.641 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001115016.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
KANSL3	NM_001115016.3	MANE Select	c.2616+87A>G	intron	N/A	NP_001108488.1
KANSL3	NM_001349256.2		c.2694+87A>G	intron	N/A	NP_001336185.1
KANSL3	NM_001349257.2		c.2694+87A>G	intron	N/A	NP_001336186.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
KANSL3	ENST00000431828.6	TSL:1 MANE Select	c.2616+87A>G	intron	N/A	ENSP00000396749.1
KANSL3	ENST00000354204.10	TSL:1	n.*2458+87A>G	intron	N/A	ENSP00000346144.7
KANSL3	ENST00000420155.5	TSL:1	n.*128+87A>G	intron	N/A	ENSP00000414426.1

Frequencies

GnomAD3 genomes

AF:

0.243

AC:

36934

AN:

152100

Hom.:

5985

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0848

Gnomad AMI

AF:

0.207

Gnomad AMR

AF:

0.400

Gnomad ASJ

AF:

0.313

Gnomad EAS

AF:

0.437

Gnomad SAS

AF:

0.659

Gnomad FIN

AF:

0.193

Gnomad MID

AF:

0.351

Gnomad NFE

AF:

0.262

Gnomad OTH

AF:

0.294

GnomAD2 exomes

AF:

0.347

AC:

53117

AN:

153230

AF XY:

0.356

show subpopulations

Gnomad AFR exome

AF:

0.0784

Gnomad AMR exome

AF:

0.564

Gnomad ASJ exome

AF:

0.308

Gnomad EAS exome

AF:

0.427

Gnomad FIN exome

AF:

0.201

Gnomad NFE exome

AF:

0.259

Gnomad OTH exome

AF:

0.346

GnomAD4 exome

AF:

0.289

AC:

394503

AN:

1366514

Hom.:

66115

Cov.:

AF XY:

0.300

AC XY:

201278

AN XY:

671650

show subpopulations

African (AFR)

AF:

0.0795

AC:

2442

AN:

30724

American (AMR)

AF:

0.541

AC:

16501

AN:

30510

Ashkenazi Jewish (ASJ)

AF:

0.315

AC:

6758

AN:

21424

East Asian (EAS)

AF:

0.469

AC:

17639

AN:

37578

South Asian (SAS)

AF:

0.660

AC:

47735

AN:

72370

European-Finnish (FIN)

AF:

0.198

AC:

8738

AN:

44082

Middle Eastern (MID)

AF:

0.421

AC:

2282

AN:

5416

European-Non Finnish (NFE)

AF:

0.257

AC:

274671

AN:

1067902

Other (OTH)

AF:

0.314

AC:

17737

AN:

56508

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.475

Heterozygous variant carriers

11714

23429

35143

46858

58572

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

9766

19532

29298

39064

48830

<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:

0.243

AC:

36967

AN:

152218

Hom.:

6002

Cov.:

AF XY:

0.249

AC XY:

18516

AN XY:

74420

show subpopulations

African (AFR)

AF:

0.0848

AC:

3522

AN:

41550

American (AMR)

AF:

0.400

AC:

6116

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.313

AC:

1087

AN:

3470

East Asian (EAS)

AF:

0.437

AC:

2260

AN:

5172

South Asian (SAS)

AF:

0.660

AC:

3186

AN:

4828

European-Finnish (FIN)

AF:

0.193

AC:

2051

AN:

10600

Middle Eastern (MID)

AF:

0.357

AC:

105

AN:

294

European-Non Finnish (NFE)

AF:

0.262

AC:

17818

AN:

67998

Other (OTH)

AF:

0.300

AC:

634

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.497

Heterozygous variant carriers

1302

2604

3906

5208

6510

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

400

800

1200

1600

2000

<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:

0.191

Hom.:

803

Bravo

AF:

0.249

Asia WGS

AF:

0.545

AC:

1890

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

0.0050

(source)

DANN

Benign

0.45

PhyloP100

-2.4

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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