rs35955962

Positions:

• chr22-26669261-G-A

Variant summary

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

The ENST00000613780.4(MIAT):​n.2929G>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 0.117 in 398,564 control chromosomes in the GnomAD database, including 2,944 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 0.11 (971 hom., cov: 33)
  • Exomes 𝑓: 0.12 (1973 hom.)
• Consequence: MIAT ENST00000613780.4 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.228

Genes affected

MIAT (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.13 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MIAT	NR_003491.4	n.2861G>A		non_coding_transcript_exon_variant	5/5
MIAT	NR_033319.3	n.2735G>A		non_coding_transcript_exon_variant	4/4
MIAT	NR_033320.3	n.2787G>A		non_coding_transcript_exon_variant	5/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MIAT	ENST00000613780.4	n.2929G>A		non_coding_transcript_exon_variant	5/5	1
MIAT	ENST00000616213.4	n.2729G>A		non_coding_transcript_exon_variant	4/4	1
MIAT	ENST00000616469.4	n.2855G>A		non_coding_transcript_exon_variant	4/4	1

Frequencies

GnomAD3 genomes AF: 0.106 AC: 16064 AN: 152102 Hom.: 969 Cov.: 33

Gnomad AFR AF: 0.0543

Gnomad AMI AF: 0.261

Gnomad AMR AF: 0.0845

Gnomad ASJ AF: 0.129

Gnomad EAS AF: 0.102

Gnomad SAS AF: 0.0825

Gnomad FIN AF: 0.157

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.132

Gnomad OTH AF: 0.0974

GnomAD4 exome AF: 0.124 AC: 30449 AN: 246344 Hom.: 1973 Cov.: 0 AF XY: 0.125 AC XY: 15611 AN XY: 124826

Gnomad4 AFR exome AF: 0.0553

Gnomad4 AMR exome AF: 0.0705

Gnomad4 ASJ exome AF: 0.117

Gnomad4 EAS exome AF: 0.0709

Gnomad4 SAS exome AF: 0.0841

Gnomad4 FIN exome AF: 0.157

Gnomad4 NFE exome AF: 0.134

Gnomad4 OTH exome AF: 0.124

GnomAD4 genome AF: 0.106 AC: 16069 AN: 152220 Hom.: 971 Cov.: 33 AF XY: 0.107 AC XY: 7953 AN XY: 74428

Gnomad4 AFR AF: 0.0541

Gnomad4 AMR AF: 0.0842

Gnomad4 ASJ AF: 0.129

Gnomad4 EAS AF: 0.102

Gnomad4 SAS AF: 0.0834

Gnomad4 FIN AF: 0.157

Gnomad4 NFE AF: 0.133

Gnomad4 OTH AF: 0.0964

Alfa AF: 0.111 Hom.: 135

Bravo AF: 0.0984

Asia WGS AF: 0.0820 AC: 285 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.3
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs35955962; hg19: chr22-27065224;