chr22-26855404-T-C

Variant names:

• chr22-26855404-T-C
• rs136544
• ENST00000450963.6:n.1375+3289T>C

Variant summary

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

The ENST00000716994.1(MIATNB):​n.886+3300T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.739 in 152,058 control chromosomes in the GnomAD database, including 41,850 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 0.74 (41850 hom., cov: 31)
• Consequence: MIATNB ENST00000716994.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.189
• Publications: 3 publications found

Genes affected

MIATNB (HGNC:50731): (MIAT neighbor)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.798 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000716994.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIATNB	ENST00000450963.6	TSL:5	n.1375+3289T>C		intron	N/A
	MIATNB	ENST00000716994.1		n.886+3300T>C		intron	N/A
	MIATNB	ENST00000716995.1		n.705-6578T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.739 AC: 112312 AN: 151940 Hom.: 41803 Cov.: 31

Gnomad AFR AF: 0.805

Gnomad AMI AF: 0.726

Gnomad AMR AF: 0.759

Gnomad ASJ AF: 0.726

Gnomad EAS AF: 0.680

Gnomad SAS AF: 0.739

Gnomad FIN AF: 0.714

Gnomad MID AF: 0.712

Gnomad NFE AF: 0.704

Gnomad OTH AF: 0.729

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

GnomAD4 genome AF: 0.739 AC: 112416 AN: 152058 Hom.: 41850 Cov.: 31 AF XY: 0.739 AC XY: 54964 AN XY: 74332

African (AFR) AF: 0.805 AC: 33410 AN: 41478

American (AMR) AF: 0.758 AC: 11586 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.726 AC: 2520 AN: 3470

East Asian (EAS) AF: 0.680 AC: 3518 AN: 5176

South Asian (SAS) AF: 0.741 AC: 3568 AN: 4814

European-Finnish (FIN) AF: 0.714 AC: 7544 AN: 10568

Middle Eastern (MID) AF: 0.704 AC: 207 AN: 294

European-Non Finnish (NFE) AF: 0.704 AC: 47863 AN: 67958

Other (OTH) AF: 0.729 AC: 1541 AN: 2114

Alfa AF: 0.721 Hom.: 6921

Bravo AF: 0.742

Asia WGS AF: 0.713 AC: 2475 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	13
DANN	Benign	0.61
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs136544; hg19: chr22-27251367;