X-76922213-G-T

Variant names:

• chrX-76922213-G-T
• rs232957
• ENST00000630388.2:n.411+85063C>A

Variant summary

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

The ENST00000630388.2(MIR325HG):​n.411+85063C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.603 in 109,973 control chromosomes in the GnomAD database, including 17,559 homozygotes. There are 19,480 hemizygotes in GnomAD. 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 0.60 (17559 hom., 19480 hem., cov: 23)
• Consequence: MIR325HG ENST00000630388.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.140
• Publications: 2 publications found

Genes affected

MIR325HG (HGNC:50346): (MIR325 host gene)

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 (NFE) allele frequency at 95% confidence interval = 0.822 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000630388.2. 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
	MIR325HG	NR_110400.2		n.306+92014C>A		intron	N/A
	MIR325HG	NR_110401.2		n.411+85063C>A		intron	N/A
	MIR325HG	NR_110402.2		n.411+85063C>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR325HG	ENST00000630388.2	TSL:1	n.411+85063C>A		intron	N/A
	MIR325HG	ENST00000626742.1	TSL:4	n.381+85063C>A		intron	N/A
	MIR325HG	ENST00000626832.1	TSL:4	n.242+92014C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.604 AC: 66343 AN: 109925 Hom.: 17572 Cov.: 23

Gnomad AFR AF: 0.179

Gnomad AMI AF: 0.926

Gnomad AMR AF: 0.616

Gnomad ASJ AF: 0.814

Gnomad EAS AF: 0.209

Gnomad SAS AF: 0.658

Gnomad FIN AF: 0.830

Gnomad MID AF: 0.763

Gnomad NFE AF: 0.828

Gnomad OTH AF: 0.639

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

GnomAD4 genome AF: 0.603 AC: 66340 AN: 109973 Hom.: 17559 Cov.: 23 AF XY: 0.604 AC XY: 19480 AN XY: 32277

African (AFR) AF: 0.179 AC: 5423 AN: 30380

American (AMR) AF: 0.616 AC: 6284 AN: 10197

Ashkenazi Jewish (ASJ) AF: 0.814 AC: 2137 AN: 2624

East Asian (EAS) AF: 0.209 AC: 723 AN: 3466

South Asian (SAS) AF: 0.661 AC: 1686 AN: 2549

European-Finnish (FIN) AF: 0.830 AC: 4733 AN: 5701

Middle Eastern (MID) AF: 0.758 AC: 163 AN: 215

European-Non Finnish (NFE) AF: 0.828 AC: 43618 AN: 52674

Other (OTH) AF: 0.635 AC: 945 AN: 1489

Alfa AF: 0.766 Hom.: 44588

Bravo AF: 0.563

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.18
DANN	Benign	0.25
PhyloP100		-0.14

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs232957;

hg19: chrX-76142638;