22-26925209-T-C

Variant names:

• chr22-26925209-T-C
• rs2213758
• ENST00000450963.6:n.1500-60948T>C

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000450963.6(MIATNB):​n.1500-60948T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.561 in 152,104 control chromosomes in the GnomAD database, including 27,325 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 0.56 (27325 hom., cov: 32)
• Consequence: MIATNB ENST00000450963.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.258
• Publications: 2 publications found

Genes affected

MIATNB (HGNC:50731): (MIAT neighbor)

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.35).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.879 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000450963.6. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIATNB	ENST00000450963.6	TSL:5	n.1500-60948T>C		intron	N/A
	MIATNB	ENST00000670559.1		n.336-24490T>C		intron	N/A
	MIATNB	ENST00000716996.1		n.820-50474T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.561 AC: 85272 AN: 151986 Hom.: 27265 Cov.: 32

Gnomad AFR AF: 0.886

Gnomad AMI AF: 0.382

Gnomad AMR AF: 0.484

Gnomad ASJ AF: 0.379

Gnomad EAS AF: 0.597

Gnomad SAS AF: 0.491

Gnomad FIN AF: 0.481

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.408

Gnomad OTH AF: 0.533

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.561 AC: 85393 AN: 152104 Hom.: 27325 Cov.: 32 AF XY: 0.561 AC XY: 41716 AN XY: 74338

African (AFR) AF: 0.887 AC: 36803 AN: 41508

American (AMR) AF: 0.485 AC: 7413 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.379 AC: 1316 AN: 3470

East Asian (EAS) AF: 0.597 AC: 3093 AN: 5178

South Asian (SAS) AF: 0.490 AC: 2361 AN: 4816

European-Finnish (FIN) AF: 0.481 AC: 5079 AN: 10552

Middle Eastern (MID) AF: 0.469 AC: 138 AN: 294

European-Non Finnish (NFE) AF: 0.408 AC: 27720 AN: 67978

Other (OTH) AF: 0.531 AC: 1122 AN: 2112

Alfa AF: 0.517 Hom.: 7214

Bravo AF: 0.578

Asia WGS AF: 0.555 AC: 1931 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.35
CADD	Benign	14
DANN	Benign	0.78
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs2213758; hg19: chr22-27321172;