rs2331311

Variant names:

• chr22-26869559-G-A
• rs2331311
• ENST00000450963.6:n.1499+7454G>A

Variant summary

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

The NR_146604.1(LOC110091768):​n.794+7454G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0358 in 152,308 control chromosomes in the GnomAD database, including 161 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 0.036 (161 hom., cov: 32)
• Consequence: LOC110091768 NR_146604.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0970
• Publications: 0 publications found

Genes affected

MIATNB (HGNC:50731): (MIAT neighbor)

LOC110091768 (HGNC:):

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 (AFR) allele frequency at 95% confidence interval = 0.0775 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_146604.1. 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
	LOC110091768	NR_146604.1		n.794+7454G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIATNB	ENST00000450963.6	TSL:5	n.1499+7454G>A		intron	N/A
	MIATNB	ENST00000653531.1		n.2221-479G>A		intron	N/A
	MIATNB	ENST00000658323.1		n.340+7454G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0358 AC: 5448 AN: 152192 Hom.: 160 Cov.: 32

Gnomad AFR AF: 0.0799

Gnomad AMI AF: 0.0757

Gnomad AMR AF: 0.0298

Gnomad ASJ AF: 0.00923

Gnomad EAS AF: 0.000384

Gnomad SAS AF: 0.0151

Gnomad FIN AF: 0.00395

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0203

Gnomad OTH AF: 0.0354

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

GnomAD4 genome AF: 0.0358 AC: 5455 AN: 152308 Hom.: 161 Cov.: 32 AF XY: 0.0343 AC XY: 2556 AN XY: 74496

African (AFR) AF: 0.0798 AC: 3316 AN: 41568

American (AMR) AF: 0.0298 AC: 456 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.00923 AC: 32 AN: 3468

East Asian (EAS) AF: 0.000385 AC: 2 AN: 5192

South Asian (SAS) AF: 0.0154 AC: 74 AN: 4818

European-Finnish (FIN) AF: 0.00395 AC: 42 AN: 10624

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0203 AC: 1379 AN: 68020

Other (OTH) AF: 0.0351 AC: 74 AN: 2110

Alfa AF: 0.0351 Hom.: 30

Bravo AF: 0.0396

Asia WGS AF: 0.0110 AC: 37 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.92
DANN	Benign	0.30
PhyloP100		-0.097

Splicing

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

Other links and lift over

dbSNP: rs2331311; hg19: chr22-27265522;