22-26850107-T-C

Variant names:

• chr22-26850107-T-C
• rs136535
• ENST00000450963.6:n.1169-1802T>C

Variant summary

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

The ENST00000716994.1(MIATNB):​n.691-1802T>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 152,060 control chromosomes in the GnomAD database, including 41,835 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 (41835 hom., cov: 31)
• Consequence: MIATNB ENST00000716994.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.85
• Publications: 5 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=-1.0).
• 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.1169-1802T>C		intron	N/A
	MIATNB	ENST00000716994.1		n.691-1802T>C		intron	N/A
	MIATNB	ENST00000716995.1		n.705-11875T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.739 AC: 112285 AN: 151944 Hom.: 41788 Cov.: 31

Gnomad AFR AF: 0.806

Gnomad AMI AF: 0.724

Gnomad AMR AF: 0.759

Gnomad ASJ AF: 0.726

Gnomad EAS AF: 0.679

Gnomad SAS AF: 0.737

Gnomad FIN AF: 0.713

Gnomad MID AF: 0.712

Gnomad NFE AF: 0.704

Gnomad OTH AF: 0.728

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

GnomAD4 genome AF: 0.739 AC: 112389 AN: 152060 Hom.: 41835 Cov.: 31 AF XY: 0.739 AC XY: 54936 AN XY: 74306

African (AFR) AF: 0.806 AC: 33419 AN: 41478

American (AMR) AF: 0.759 AC: 11600 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.726 AC: 2518 AN: 3466

East Asian (EAS) AF: 0.678 AC: 3493 AN: 5150

South Asian (SAS) AF: 0.739 AC: 3559 AN: 4816

European-Finnish (FIN) AF: 0.713 AC: 7537 AN: 10570

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

European-Non Finnish (NFE) AF: 0.704 AC: 47859 AN: 67980

Other (OTH) AF: 0.728 AC: 1537 AN: 2110

Alfa AF: 0.713 Hom.: 33519

Bravo AF: 0.742

Asia WGS AF: 0.714 AC: 2480 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.016
DANN	Benign	0.51
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs136535; hg19: chr22-27246070;