rs739259

Variant names:

• chr22-26960616-A-G
• rs739259
• ENST00000450963.6:n.1500-25541A>G

Variant summary

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

The ENST00000450963.6(MIATNB):​n.1500-25541A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.417 in 151,912 control chromosomes in the GnomAD database, including 13,660 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 0.42 (13660 hom., cov: 31)
• Consequence: MIATNB ENST00000450963.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.338
• Publications: 8 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=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.56 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.1500-25541A>G		intron_variant	Intron 11 of 13	5
MIATNB	ENST00000670559.1	n.462-7125A>G		intron_variant	Intron 3 of 3
MIATNB	ENST00000716996.1	n.820-15067A>G		intron_variant	Intron 7 of 8

Frequencies

GnomAD3 genomes AF: 0.417 AC: 63335 AN: 151794 Hom.: 13648 Cov.: 31

Gnomad AFR AF: 0.496

Gnomad AMI AF: 0.260

Gnomad AMR AF: 0.457

Gnomad ASJ AF: 0.396

Gnomad EAS AF: 0.578

Gnomad SAS AF: 0.343

Gnomad FIN AF: 0.413

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.358

Gnomad OTH AF: 0.422

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

GnomAD4 genome AF: 0.417 AC: 63396 AN: 151912 Hom.: 13660 Cov.: 31 AF XY: 0.419 AC XY: 31075 AN XY: 74252

African (AFR) AF: 0.496 AC: 20523 AN: 41408

American (AMR) AF: 0.457 AC: 6982 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.396 AC: 1373 AN: 3466

East Asian (EAS) AF: 0.578 AC: 2969 AN: 5140

South Asian (SAS) AF: 0.343 AC: 1647 AN: 4806

European-Finnish (FIN) AF: 0.413 AC: 4369 AN: 10576

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.358 AC: 24330 AN: 67938

Other (OTH) AF: 0.421 AC: 888 AN: 2108

Alfa AF: 0.382 Hom.: 19184

Bravo AF: 0.434

Asia WGS AF: 0.439 AC: 1529 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.6
DANN	Benign	0.46
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs739259; hg19: chr22-27356579; COSMIC: COSV99805412;