2-96602175-C-G

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4

The NM_001115016.3(KANSL3):​c.2423G>C​(p.Gly808Ala) variant causes a missense change. The variant allele was found at a frequency of 0.00000689 in 1,450,820 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G808V) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 32)
Exomes š‘“: 0.0000069 ( 0 hom. )

Consequence

KANSL3
NM_001115016.3 missense

Scores

2
7
8

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 7.17
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 1 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.3879796).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
KANSL3NM_001115016.3 linkc.2423G>C p.Gly808Ala missense_variant Exon 19 of 21 ENST00000431828.6 NP_001108488.1 Q9P2N6-3

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
KANSL3ENST00000431828.6 linkc.2423G>C p.Gly808Ala missense_variant Exon 19 of 21 1 NM_001115016.3 ENSP00000396749.1 Q9P2N6-3

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD3 exomes
AF:
0.00000867
AC:
2
AN:
230656
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
124602
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000192
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.00000689
AC:
10
AN:
1450820
Hom.:
0
Cov.:
32
AF XY:
0.00000833
AC XY:
6
AN XY:
720394
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000903
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
0.43
BayesDel_addAF
Uncertain
0.045
T
BayesDel_noAF
Benign
-0.15
CADD
Pathogenic
27
DANN
Uncertain
1.0
Eigen
Uncertain
0.26
Eigen_PC
Uncertain
0.36
FATHMM_MKL
Pathogenic
0.99
D
LIST_S2
Uncertain
0.97
D
M_CAP
Benign
0.029
D
MetaRNN
Benign
0.39
T
MetaSVM
Benign
-0.72
T
PrimateAI
Pathogenic
0.81
D
PROVEAN
Benign
-2.0
N
REVEL
Benign
0.20
Sift
Uncertain
0.014
D
Sift4G
Benign
0.20
T
Polyphen
0.95
P
Vest4
0.52
MVP
0.22
MPC
0.81
ClinPred
0.81
D
GERP RS
4.8
gMVP
0.65

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: rs1163005706; hg19: chr2-97267912; API