X-76962159-T-G

Position:

• chrX-76962159-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000630388.2(MIR325HG):​n.411+45117A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.601 in 110,603 control chromosomes in the GnomAD database, including 17,555 homozygotes. There are 19,632 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 (17555 hom., 19632 hem., cov: 23)
• Consequence: MIR325HG ENST00000630388.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.312

Genes affected

MIR325HG (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.821 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MIR325HG	NR_110400.2	n.306+52068A>C		intron_variant
MIR325HG	NR_110401.2	n.411+45117A>C		intron_variant
MIR325HG	NR_110402.2	n.411+45117A>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MIR325HG	ENST00000630388.2	n.411+45117A>C		intron_variant		1
MIR325HG	ENST00000626742.1	n.381+45117A>C		intron_variant		4
MIR325HG	ENST00000626832.1	n.242+52068A>C		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.602 AC: 66514 AN: 110552 Hom.: 17568 Cov.: 23 AF XY: 0.598 AC XY: 19608 AN XY: 32810

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.927

Gnomad AMR AF: 0.613

Gnomad ASJ AF: 0.811

Gnomad EAS AF: 0.209

Gnomad SAS AF: 0.654

Gnomad FIN AF: 0.832

Gnomad MID AF: 0.773

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: 0.601 AC: 66513 AN: 110603 Hom.: 17555 Cov.: 23 AF XY: 0.597 AC XY: 19632 AN XY: 32871

Gnomad4 AFR AF: 0.178

Gnomad4 AMR AF: 0.614

Gnomad4 ASJ AF: 0.811

Gnomad4 EAS AF: 0.209

Gnomad4 SAS AF: 0.657

Gnomad4 FIN AF: 0.832

Gnomad4 NFE AF: 0.828

Gnomad4 OTH AF: 0.635

Alfa AF: 0.736 Hom.: 17462

Bravo AF: 0.563

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.4
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4892718; hg19: chrX-76182584;