NM_152519.4:c.2040T>C

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate

The NM_152519.4(KANSL1L):​c.2040T>C​(p.Thr680Thr) variant causes a synonymous change. The variant allele was found at a frequency of 0.000313 in 1,539,198 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.00021 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00032 ( 0 hom. )

Consequence

KANSL1L
NM_152519.4 synonymous

Scores

2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 3.77
Variant links:
Genes affected
KANSL1L (HGNC:26310): (KAT8 regulatory NSL complex subunit 1 like) Predicted to enable histone acetyltransferase binding activity. Predicted to be part of NSL complex. [provided by Alliance of Genome Resources, Apr 2022]
KANSL1L-AS1 (HGNC:41139): (KANSL1L antisense RNA 1)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.59).
BP6
Variant 2-210031536-A-G is Benign according to our data. Variant chr2-210031536-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 735231.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
KANSL1LNM_152519.4 linkc.2040T>C p.Thr680Thr synonymous_variant Exon 9 of 15 ENST00000281772.14 NP_689732.2 A0AUZ9-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
KANSL1LENST00000281772.14 linkc.2040T>C p.Thr680Thr synonymous_variant Exon 9 of 15 5 NM_152519.4 ENSP00000281772.8 A0AUZ9-1
KANSL1LENST00000418791.5 linkc.2030-1618T>C intron_variant Intron 8 of 13 1 ENSP00000405724.1 A0AUZ9-2
KANSL1L-AS1ENST00000452057.1 linkn.775+29A>G intron_variant Intron 1 of 3 2
KANSL1L-AS1ENST00000668130.1 linkn.936+29A>G intron_variant Intron 1 of 2

Frequencies

GnomAD3 genomes
AF:
0.000210
AC:
32
AN:
152172
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0000724
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000262
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000368
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.000114
AC:
27
AN:
236846
Hom.:
0
AF XY:
0.0000936
AC XY:
12
AN XY:
128186
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:
0.000245
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.000324
AC:
450
AN:
1386908
Hom.:
0
Cov.:
24
AF XY:
0.000312
AC XY:
216
AN XY:
693330
show subpopulations
Gnomad4 AFR exome
AF:
0.0000964
Gnomad4 AMR exome
AF:
0.000101
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:
0.000412
Gnomad4 OTH exome
AF:
0.000138
GnomAD4 genome
AF:
0.000210
AC:
32
AN:
152290
Hom.:
0
Cov.:
32
AF XY:
0.000134
AC XY:
10
AN XY:
74482
show subpopulations
Gnomad4 AFR
AF:
0.0000722
Gnomad4 AMR
AF:
0.000261
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000368
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.000281
Hom.:
0
Bravo
AF:
0.000280
EpiCase
AF:
0.000383
EpiControl
AF:
0.000237

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Nov 02, 2017
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.59
CADD
Benign
9.3
DANN
Benign
0.88

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.060
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: rs143376566; hg19: chr2-210896260; API