11-65497960-C-G

Position:

• chr11-65497960-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_002819.4(MALAT1):​n.223C>G 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 0.00221 in 518,968 control chromosomes in the GnomAD database, including 28 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 0.0020 (9 hom., cov: 32)
  • Exomes 𝑓: 0.0023 (19 hom.)
• Consequence: MALAT1 NR_002819.4 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16

Genes affected

MALAT1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAdExome4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0506 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MALAT1	NR_002819.4	n.223C>G		non_coding_transcript_exon_variant	1/1
MALAT1	NR_144567.1	n.223C>G		non_coding_transcript_exon_variant	1/2
MALAT1	NR_144568.1	n.223C>G		non_coding_transcript_exon_variant	1/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MALAT1	ENST00000534336.3	n.321C>G		non_coding_transcript_exon_variant	1/1	6
MALAT1	ENST00000619449.3	n.178+95C>G		intron_variant		3
MALAT1	ENST00000710852.1	n.158+95C>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.00201 AC: 306 AN: 152202 Hom.: 9 Cov.: 32

Gnomad AFR AF: 0.0000482

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000262

Gnomad ASJ AF: 0.000576

Gnomad EAS AF: 0.0549

Gnomad SAS AF: 0.00166

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000147

Gnomad OTH AF: 0.00192

GnomAD3 exomes AF: 0.00456 AC: 1057 AN: 231786 Hom.: 29 AF XY: 0.00405 AC XY: 518 AN XY: 127856

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.0000583

Gnomad ASJ exome AF: 0.000508

Gnomad EAS exome AF: 0.0571

Gnomad SAS exome AF: 0.00102

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000370

Gnomad OTH exome AF: 0.00187

GnomAD4 exome AF: 0.00230 AC: 842 AN: 366646 Hom.: 19 Cov.: 0 AF XY: 0.00212 AC XY: 445 AN XY: 210226

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.0000826

Gnomad4 ASJ exome AF: 0.000511

Gnomad4 EAS exome AF: 0.0539

Gnomad4 SAS exome AF: 0.00135

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0000156

Gnomad4 OTH exome AF: 0.00175

GnomAD4 genome AF: 0.00200 AC: 304 AN: 152322 Hom.: 9 Cov.: 32 AF XY: 0.00243 AC XY: 181 AN XY: 74478

Gnomad4 AFR AF: 0.0000481

Gnomad4 AMR AF: 0.000261

Gnomad4 ASJ AF: 0.000576

Gnomad4 EAS AF: 0.0546

Gnomad4 SAS AF: 0.00166

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000147

Gnomad4 OTH AF: 0.00190

Alfa AF: 0.000323 Hom.: 0

Bravo AF: 0.00231

Asia WGS AF: 0.0110 AC: 39 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.36
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11227209; hg19: chr11-65265431;