22-26646142-C-T

Variant names:

• chr22-26646142-C-T
• rs744016
• ENST00000840167.1:n.790+906G>A

Variant summary

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

The ENST00000840167.1(ENSG00000309298):​n.790+906G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.163 in 152,128 control chromosomes in the GnomAD database, including 2,176 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 0.16 (2176 hom., cov: 32)
• Consequence: ENSG00000309298 ENST00000840167.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0570
• Publications: 13 publications found

Genes affected

ENSG00000309298 (HGNC:):

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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.296 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
ENSG00000309298	ENST00000840167.1	n.790+906G>A		intron_variant	Intron 1 of 1
ENSG00000309298	ENST00000840168.1	n.214+131G>A		intron_variant	Intron 1 of 1
MIATNB	ENST00000717180.1	n.-221C>T		upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.163 AC: 24812 AN: 152010 Hom.: 2171 Cov.: 32

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.224

Gnomad AMR AF: 0.174

Gnomad ASJ AF: 0.146

Gnomad EAS AF: 0.264

Gnomad SAS AF: 0.308

Gnomad FIN AF: 0.133

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.167

Gnomad OTH AF: 0.184

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

GnomAD4 genome AF: 0.163 AC: 24846 AN: 152128 Hom.: 2176 Cov.: 32 AF XY: 0.164 AC XY: 12230 AN XY: 74362

African (AFR) AF: 0.130 AC: 5374 AN: 41492

American (AMR) AF: 0.175 AC: 2673 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.146 AC: 506 AN: 3470

East Asian (EAS) AF: 0.264 AC: 1362 AN: 5164

South Asian (SAS) AF: 0.309 AC: 1485 AN: 4810

European-Finnish (FIN) AF: 0.133 AC: 1411 AN: 10588

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.167 AC: 11355 AN: 68004

Other (OTH) AF: 0.192 AC: 405 AN: 2110

Alfa AF: 0.173 Hom.: 6890

Bravo AF: 0.165

Asia WGS AF: 0.318 AC: 1106 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.4
DANN	Benign	0.24
PhyloP100		0.057

Splicing

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

Other links and lift over

dbSNP: rs744016; hg19: chr22-27042106;