X-76922213-G-T

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIR325HG	NR_110400.2	n.306+92014C>A		intron_variant	Intron 1 of 3
MIR325HG	NR_110401.2	n.411+85063C>A		intron_variant	Intron 2 of 3
MIR325HG	NR_110402.2	n.411+85063C>A		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR325HG	ENST00000630388.2	n.411+85063C>A		intron_variant	Intron 2 of 3	1
MIR325HG	ENST00000626742.1	n.381+85063C>A		intron_variant	Intron 2 of 3	4
MIR325HG	ENST00000626832.1	n.242+92014C>A		intron_variant	Intron 1 of 2	4

Frequencies

GnomAD3 genomes AF: 0.604 AC: 66343 AN: 109925 Hom.: 17572 Cov.: 23 AF XY: 0.604 AC XY: 19458 AN XY: 32219

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

Gnomad4 AFR AF: 0.179

Gnomad4 AMR AF: 0.616

Gnomad4 ASJ AF: 0.814

Gnomad4 EAS AF: 0.209

Gnomad4 SAS AF: 0.661

Gnomad4 FIN AF: 0.830

Gnomad4 NFE AF: 0.828

Gnomad4 OTH AF: 0.635

Alfa AF: 0.775 Hom.: 36358

Bravo AF: 0.563

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs232957; hg19: chrX-76142638;