Genetic Variant MALT1-AS1:n.1154A>C (chr18-58670064-T-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000588144.2(MALT1-AS1):n.1154A>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.168 in 152,144 control chromosomes in the GnomAD database, including 2,194 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 0.17 ( 2194 hom., cov: 32)

Exomes 𝑓: 0.25 ( 0 hom. )

Consequence

MALT1-AS1
ENST00000588144.2 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.61

Publications

9 publications found

Variant links:

COSMIC-nc: COSV61934877

Genes affected

MALT1-AS1 (HGNC:55306): (MALT1 antisense RNA 1)

MALT1-AS1 links:

Genome browser will be placed here

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=-0.81).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.2 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MALT1-AS1	NR_164150.1 link	n.1150A>C		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
MALT1-AS1	ENST00000588144.2 link	n.1154A>C	non_coding_transcript_exon_variant	Exon 2 of 2	2
MALT1-AS1	ENST00000769966.1 link	n.1113A>C	non_coding_transcript_exon_variant	Exon 2 of 2
MALT1-AS1	ENST00000769967.1 link	n.1110A>C	non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.168

AC:

25498

AN:

152022

Hom.:

2193

Cov.:

show subpopulations

Gnomad AFR

AF:

0.173

Gnomad AMI

AF:

0.152

Gnomad AMR

AF:

0.206

Gnomad ASJ

AF:

0.173

Gnomad EAS

AF:

0.141

Gnomad SAS

AF:

0.111

Gnomad FIN

AF:

0.151

Gnomad MID

AF:

0.177

Gnomad NFE

AF:

0.164

Gnomad OTH

AF:

0.184

GnomAD4 exome

AF:

0.250

AC:

AN:

Hom.:

Cov.:

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.00

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.500

AC:

AN:

Other (OTH)

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.675

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.168

AC:

25505

AN:

152140

Hom.:

2194

Cov.:

AF XY:

0.167

AC XY:

12443

AN XY:

74388

show subpopulations

African (AFR)

AF:

0.173

AC:

7161

AN:

41484

American (AMR)

AF:

0.206

AC:

3153

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.173

AC:

599

AN:

3470

East Asian (EAS)

AF:

0.140

AC:

728

AN:

5182

South Asian (SAS)

AF:

0.111

AC:

534

AN:

4822

European-Finnish (FIN)

AF:

0.151

AC:

1602

AN:

10576

Middle Eastern (MID)

AF:

0.187

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.164

AC:

11151

AN:

67998

Other (OTH)

AF:

0.181

AC:

383

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1118

2236

3354

4472

5590

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

276

552

828

1104

1380

<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:

0.166

Hom.:

3686

Bravo

AF:

0.178

Asia WGS

AF:

0.124

AC:

430

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

0.53

(source)

DANN

Benign

0.53

PhyloP100

-1.6

Splicing

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over