chr11-65500727-G-A

Position:

• chr11-65500727-G-A

Variant summary

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

The ENST00000508832.3(MALAT1):​n.1686G>A 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 0.0147 in 518,992 control chromosomes in the GnomAD database, including 406 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 0.035 (295 hom., cov: 32)
  • Exomes 𝑓: 0.0060 (111 hom.)
• Consequence: MALAT1 ENST00000508832.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.556

Genes affected

MALAT1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.118 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MALAT1	NR_002819.4	n.2990G>A		non_coding_transcript_exon_variant	1/1
MALAT1	NR_144567.1	n.2756G>A		non_coding_transcript_exon_variant	2/2
MALAT1	NR_144568.1	n.2756G>A		non_coding_transcript_exon_variant	2/3
TALAM1	NR_145459.1	n.6706C>T		non_coding_transcript_exon_variant	1/1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MALAT1	ENST00000508832.3	n.1686G>A		non_coding_transcript_exon_variant	1/2	2
MALAT1	ENST00000534336.3	n.3088G>A		non_coding_transcript_exon_variant	1/1	6
MALAT1	ENST00000610851.2	n.1669G>A		non_coding_transcript_exon_variant	1/2	2

Frequencies

GnomAD3 genomes AF: 0.0354 AC: 5390 AN: 152158 Hom.: 294 Cov.: 32

Gnomad AFR AF: 0.120

Gnomad AMI AF: 0.00658

Gnomad AMR AF: 0.0148

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00692

Gnomad SAS AF: 0.00228

Gnomad FIN AF: 0.000282

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.000941

Gnomad OTH AF: 0.0240

GnomAD3 exomes AF: 0.00992 AC: 2300 AN: 231870 Hom.: 124 AF XY: 0.00807 AC XY: 1032 AN XY: 127896

Gnomad AFR exome AF: 0.126

Gnomad AMR exome AF: 0.00632

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00580

Gnomad SAS exome AF: 0.00294

Gnomad FIN exome AF: 0.000515

Gnomad NFE exome AF: 0.000822

Gnomad OTH exome AF: 0.00613

GnomAD4 exome AF: 0.00600 AC: 2202 AN: 366716 Hom.: 111 Cov.: 0 AF XY: 0.00494 AC XY: 1039 AN XY: 210268

Gnomad4 AFR exome AF: 0.130

Gnomad4 AMR exome AF: 0.00606

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00721

Gnomad4 SAS exome AF: 0.00313

Gnomad4 FIN exome AF: 0.000532

Gnomad4 NFE exome AF: 0.000672

Gnomad4 OTH exome AF: 0.00969

GnomAD4 genome AF: 0.0355 AC: 5402 AN: 152276 Hom.: 295 Cov.: 32 AF XY: 0.0350 AC XY: 2606 AN XY: 74468

Gnomad4 AFR AF: 0.120

Gnomad4 AMR AF: 0.0148

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00693

Gnomad4 SAS AF: 0.00228

Gnomad4 FIN AF: 0.000282

Gnomad4 NFE AF: 0.000941

Gnomad4 OTH AF: 0.0237

Alfa AF: 0.0154 Hom.: 27

Bravo AF: 0.0411

Asia WGS AF: 0.0170 AC: 60 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	16
DANN	Benign	0.84
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7927113; hg19: chr11-65268198;