ENST00000588144.2:n.1154A>C

Variant names:

• chr18-58670064-T-G
• rs12458537
• ENST00000588144.2:n.1154A>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.61
• Publications: 9 publications found

Genes affected

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

ACMG classification

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000588144.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MALT1-AS1	NR_164150.1		n.1150A>C		non_coding_transcript_exon	Exon 2 of 2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MALT1-AS1	ENST00000588144.2	TSL:2	n.1154A>C		non_coding_transcript_exon	Exon 2 of 2
	MALT1-AS1	ENST00000769966.1		n.1113A>C		non_coding_transcript_exon	Exon 2 of 2
	MALT1-AS1	ENST00000769967.1		n.1110A>C		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.168 AC: 25498 AN: 152022 Hom.: 2193 Cov.: 32

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: 1 AN: 4 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.500 AC: 1 AN: 2

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.168 AC: 25505 AN: 152140 Hom.: 2194 Cov.: 32 AF XY: 0.167 AC XY: 12443 AN XY: 74388

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: 55 AN: 294

European-Non Finnish (NFE) AF: 0.164 AC: 11151 AN: 67998

Other (OTH) AF: 0.181 AC: 383 AN: 2114

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.53
DANN	Benign	0.53
PhyloP100		-1.6

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs12458537; hg19: chr18-56337296; COSMIC: COSV61934877;