ENST00000417083.2:n.640+1504T>C

Variant names:

• chr22-26713512-T-C
• rs5752388
• ENST00000417083.2:n.640+1504T>C

Variant summary

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

The ENST00000417083.2(MIATNB):​n.640+1504T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.29 in 151,064 control chromosomes in the GnomAD database, including 6,563 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 0.29 (6563 hom., cov: 30)
• Consequence: MIATNB ENST00000417083.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308
• 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.353 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000417083.2. 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
	MIATNB	NR_110543.1		n.146-3741T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIATNB	ENST00000417083.2	TSL:3	n.640+1504T>C		intron	N/A
	MIATNB	ENST00000421253.1	TSL:3	n.133-3741T>C		intron	N/A
	MIATNB	ENST00000435162.5	TSL:2	n.184-3741T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.290 AC: 43807 AN: 150944 Hom.: 6544 Cov.: 30

Gnomad AFR AF: 0.340

Gnomad AMI AF: 0.299

Gnomad AMR AF: 0.360

Gnomad ASJ AF: 0.254

Gnomad EAS AF: 0.362

Gnomad SAS AF: 0.339

Gnomad FIN AF: 0.273

Gnomad MID AF: 0.325

Gnomad NFE AF: 0.239

Gnomad OTH AF: 0.301

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

GnomAD4 genome AF: 0.290 AC: 43874 AN: 151064 Hom.: 6563 Cov.: 30 AF XY: 0.295 AC XY: 21714 AN XY: 73638

African (AFR) AF: 0.340 AC: 14088 AN: 41396

American (AMR) AF: 0.361 AC: 5503 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.254 AC: 879 AN: 3466

East Asian (EAS) AF: 0.361 AC: 1844 AN: 5114

South Asian (SAS) AF: 0.338 AC: 1625 AN: 4808

European-Finnish (FIN) AF: 0.273 AC: 2690 AN: 9846

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.239 AC: 16220 AN: 67866

Other (OTH) AF: 0.309 AC: 653 AN: 2110

Alfa AF: 0.256 Hom.: 21686

Bravo AF: 0.300

Asia WGS AF: 0.385 AC: 1339 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.2
DANN	Benign	0.75
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs5752388; hg19: chr22-27109475;