rs5938679

Positions:

• chrX-76783047-A-C
• chrX-76783047-A-G

Variant summary

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

The ENST00000630388.2(MIR325HG):​n.412-89960T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.141 in 109,829 control chromosomes in the GnomAD database, including 866 homozygotes. There are 4,037 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 0.14 (866 hom., 4037 hem., cov: 22)
• Consequence: MIR325HG ENST00000630388.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.55

Genes affected

MIR325HG (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.156 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MIR325HG	NR_110400.2	n.307-89960T>G		intron_variant
MIR325HG	NR_110401.2	n.412-124379T>G		intron_variant
MIR325HG	NR_110402.2	n.412-89960T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MIR325HG	ENST00000630388.2	n.412-89960T>G		intron_variant		1
MIR325HG	ENST00000626742.1	n.382-89960T>G		intron_variant		4
MIR325HG	ENST00000626832.1	n.243-124379T>G		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.141 AC: 15453 AN: 109779 Hom.: 866 Cov.: 22 AF XY: 0.126 AC XY: 4038 AN XY: 32103

Gnomad AFR AF: 0.146

Gnomad AMI AF: 0.0516

Gnomad AMR AF: 0.0965

Gnomad ASJ AF: 0.142

Gnomad EAS AF: 0.0247

Gnomad SAS AF: 0.0819

Gnomad FIN AF: 0.131

Gnomad MID AF: 0.147

Gnomad NFE AF: 0.159

Gnomad OTH AF: 0.138

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

GnomAD4 genome AF: 0.141 AC: 15459 AN: 109829 Hom.: 866 Cov.: 22 AF XY: 0.126 AC XY: 4037 AN XY: 32163

Gnomad4 AFR AF: 0.145

Gnomad4 AMR AF: 0.0963

Gnomad4 ASJ AF: 0.142

Gnomad4 EAS AF: 0.0251

Gnomad4 SAS AF: 0.0806

Gnomad4 FIN AF: 0.131

Gnomad4 NFE AF: 0.159

Gnomad4 OTH AF: 0.143

Alfa AF: 0.154 Hom.: 2802

Bravo AF: 0.139

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.7
DANN	Benign	0.18

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5938679; hg19: chrX-76003472;