rs141260832

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_001374828.1(ARID1B):​c.1841T>A​(p.Met614Lys) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. 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. M614I) has been classified as Likely benign.

Frequency

Genomes: not found (cov: 32)

Consequence

ARID1B
NM_001374828.1 missense

Scores

1
5
13

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 6.42
Variant links:
Genes affected
ARID1B (HGNC:18040): (AT-rich interaction domain 1B) This locus encodes an AT-rich DNA interacting domain-containing protein. The encoded protein is a component of the SWI/SNF chromatin remodeling complex and may play a role in cell-cycle activation. The protein encoded by this locus is similar to AT-rich interactive domain-containing protein 1A. These two proteins function as alternative, mutually exclusive ARID-subunits of the SWI/SNF complex. The associated complexes play opposing roles. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2016]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.23829731).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ARID1BNM_001374828.1 linkuse as main transcriptc.1841T>A p.Met614Lys missense_variant 2/20 ENST00000636930.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ARID1BENST00000636930.2 linkuse as main transcriptc.1841T>A p.Met614Lys missense_variant 2/202 NM_001374828.1 A2Q8NFD5-3

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
30
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.67
BayesDel_addAF
Benign
-0.13
T
BayesDel_noAF
Benign
-0.43
CADD
Uncertain
24
DANN
Uncertain
0.98
DEOGEN2
Benign
0.039
.;T;.;.;.;.;.;T
Eigen
Benign
-0.18
Eigen_PC
Benign
0.0030
FATHMM_MKL
Uncertain
0.95
D
LIST_S2
Uncertain
0.93
D;D;D;D;D;D;D;D
M_CAP
Benign
0.010
T
MetaRNN
Benign
0.24
T;T;T;T;T;T;T;T
MetaSVM
Benign
-0.88
T
MutationAssessor
Benign
1.4
.;L;L;L;.;.;.;.
MutationTaster
Benign
0.90
D;D;D;D
PrimateAI
Uncertain
0.71
T
PROVEAN
Benign
-1.8
.;N;.;.;.;.;.;N
REVEL
Benign
0.14
Sift
Uncertain
0.0010
.;D;.;.;.;.;.;D
Sift4G
Benign
0.94
.;T;.;.;.;.;.;T
Polyphen
0.0080, 0.014
.;B;.;B;.;.;.;.
Vest4
0.69
MutPred
0.39
.;Gain of methylation at M531 (P = 0.0087);Gain of methylation at M531 (P = 0.0087);Gain of methylation at M531 (P = 0.0087);.;.;.;.;
MVP
0.14
MPC
0.66
ClinPred
0.84
D
GERP RS
4.2
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.8
Varity_R
0.76
gMVP
0.53

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr6-157150410; API