chr22-26985874-T-C

Variant names:

• chr22-26985874-T-C
• rs4345013
• ENST00000450963.6:n.1500-283T>C

Variant summary

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

The ENST00000450963.6(MIATNB):​n.1500-283T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.265 in 152,006 control chromosomes in the GnomAD database, including 5,777 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 0.27 (5777 hom., cov: 32)
• Consequence: MIATNB ENST00000450963.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07
• Publications: 4 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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.344 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIATNB	ENST00000450963.6	n.1500-283T>C		intron_variant	Intron 11 of 13	5
MIATNB	ENST00000717151.1	n.500-283T>C		intron_variant	Intron 4 of 6
MIATNB	ENST00000717152.1	n.701-3190T>C		intron_variant	Intron 4 of 5
MIATNB	ENST00000717153.1	n.346-17593T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.265 AC: 40247 AN: 151886 Hom.: 5771 Cov.: 32

Gnomad AFR AF: 0.349

Gnomad AMI AF: 0.354

Gnomad AMR AF: 0.279

Gnomad ASJ AF: 0.176

Gnomad EAS AF: 0.199

Gnomad SAS AF: 0.325

Gnomad FIN AF: 0.149

Gnomad MID AF: 0.248

Gnomad NFE AF: 0.234

Gnomad OTH AF: 0.252

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

GnomAD4 genome AF: 0.265 AC: 40289 AN: 152006 Hom.: 5777 Cov.: 32 AF XY: 0.262 AC XY: 19445 AN XY: 74288

African (AFR) AF: 0.349 AC: 14465 AN: 41444

American (AMR) AF: 0.279 AC: 4256 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.176 AC: 610 AN: 3468

East Asian (EAS) AF: 0.198 AC: 1025 AN: 5164

South Asian (SAS) AF: 0.324 AC: 1553 AN: 4796

European-Finnish (FIN) AF: 0.149 AC: 1578 AN: 10586

Middle Eastern (MID) AF: 0.226 AC: 66 AN: 292

European-Non Finnish (NFE) AF: 0.234 AC: 15877 AN: 67974

Other (OTH) AF: 0.255 AC: 537 AN: 2108

Alfa AF: 0.243 Hom.: 7774

Bravo AF: 0.278

Asia WGS AF: 0.284 AC: 987 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.22
DANN	Benign	0.80
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs4345013; hg19: chr22-27381837;