chr22-26814728-A-G

Variant names:

• chr22-26814728-A-G
• rs713974
• ENST00000450963.6:n.1168+24020A>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000450963.6(MIATNB):​n.1168+24020A>G variant causes a intron change. The variant allele was found at a frequency of 0.728 in 152,136 control chromosomes in the GnomAD database, including 40,658 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 0.73 (40658 hom., cov: 33)
• Consequence: MIATNB ENST00000450963.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.80
• Publications: 3 publications found

Genes affected

MIATNB (HGNC:50731): (MIAT neighbor)

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.24).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.775 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.1168+24020A>G		intron_variant	Intron 9 of 13	5
MIATNB	ENST00000716994.1	n.690+36143A>G		intron_variant	Intron 5 of 8
MIATNB	ENST00000716995.1	n.704+24020A>G		intron_variant	Intron 6 of 7

Frequencies

GnomAD3 genomes AF: 0.728 AC: 110704 AN: 152018 Hom.: 40625 Cov.: 33

Gnomad AFR AF: 0.671

Gnomad AMI AF: 0.758

Gnomad AMR AF: 0.720

Gnomad ASJ AF: 0.826

Gnomad EAS AF: 0.612

Gnomad SAS AF: 0.610

Gnomad FIN AF: 0.699

Gnomad MID AF: 0.725

Gnomad NFE AF: 0.781

Gnomad OTH AF: 0.753

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

GnomAD4 genome AF: 0.728 AC: 110785 AN: 152136 Hom.: 40658 Cov.: 33 AF XY: 0.722 AC XY: 53688 AN XY: 74354

African (AFR) AF: 0.671 AC: 27830 AN: 41488

American (AMR) AF: 0.720 AC: 11003 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.826 AC: 2866 AN: 3470

East Asian (EAS) AF: 0.613 AC: 3173 AN: 5178

South Asian (SAS) AF: 0.610 AC: 2942 AN: 4826

European-Finnish (FIN) AF: 0.699 AC: 7394 AN: 10576

Middle Eastern (MID) AF: 0.718 AC: 211 AN: 294

European-Non Finnish (NFE) AF: 0.781 AC: 53085 AN: 67990

Other (OTH) AF: 0.754 AC: 1590 AN: 2110

Alfa AF: 0.761 Hom.: 82551

Bravo AF: 0.725

Asia WGS AF: 0.619 AC: 2150 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.24
CADD	Benign	22
DANN	Benign	0.73
PhyloP100		3.8

Splicing

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

Other links and lift over

dbSNP: rs713974; hg19: chr22-27210691;