22-26888059-T-C

Variant names:

• chr22-26888059-T-C
• rs4242
• ENST00000450963.6:n.1499+25954T>C

Variant summary

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

The ENST00000670559.1(MIATNB):​n.335+25954T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.669 in 152,070 control chromosomes in the GnomAD database, including 34,339 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 0.67 (34339 hom., cov: 32)
• Consequence: MIATNB ENST00000670559.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.84
• 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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.834 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000670559.1. 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.1499+25954T>C		intron	N/A
	MIATNB	ENST00000670559.1		n.335+25954T>C		intron	N/A
	MIATNB	ENST00000716994.1		n.1011-18519T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.669 AC: 101679 AN: 151952 Hom.: 34322 Cov.: 32

Gnomad AFR AF: 0.624

Gnomad AMI AF: 0.587

Gnomad AMR AF: 0.747

Gnomad ASJ AF: 0.674

Gnomad EAS AF: 0.855

Gnomad SAS AF: 0.601

Gnomad FIN AF: 0.753

Gnomad MID AF: 0.649

Gnomad NFE AF: 0.657

Gnomad OTH AF: 0.687

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

GnomAD4 genome AF: 0.669 AC: 101739 AN: 152070 Hom.: 34339 Cov.: 32 AF XY: 0.676 AC XY: 50276 AN XY: 74334

African (AFR) AF: 0.624 AC: 25876 AN: 41456

American (AMR) AF: 0.747 AC: 11418 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.674 AC: 2336 AN: 3468

East Asian (EAS) AF: 0.855 AC: 4422 AN: 5174

South Asian (SAS) AF: 0.601 AC: 2895 AN: 4818

European-Finnish (FIN) AF: 0.753 AC: 7966 AN: 10574

Middle Eastern (MID) AF: 0.646 AC: 190 AN: 294

European-Non Finnish (NFE) AF: 0.657 AC: 44659 AN: 67982

Other (OTH) AF: 0.684 AC: 1444 AN: 2110

Alfa AF: 0.657 Hom.: 103710

Bravo AF: 0.667

Asia WGS AF: 0.706 AC: 2453 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.13
DANN	Benign	0.62
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs4242; hg19: chr22-27284022;