X-76783047-A-C

Variant names:

• chrX-76783047-A-C
• rs5938679
• ENST00000630388.2:n.412-89960T>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 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=-1.04).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.156 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR325HG	NR_110400.2		n.307-89960T>G		intron	N/A
	MIR325HG	NR_110401.2		n.412-124379T>G		intron	N/A
	MIR325HG	NR_110402.2		n.412-89960T>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR325HG	ENST00000630388.2	TSL:1	n.412-89960T>G		intron	N/A
	MIR325HG	ENST00000626742.1	TSL:4	n.382-89960T>G		intron	N/A
	MIR325HG	ENST00000626832.1	TSL:4	n.243-124379T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.141 AC: 15453 AN: 109779 Hom.: 866 Cov.: 22

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

African (AFR) AF: 0.145 AC: 4385 AN: 30147

American (AMR) AF: 0.0963 AC: 988 AN: 10260

Ashkenazi Jewish (ASJ) AF: 0.142 AC: 370 AN: 2614

East Asian (EAS) AF: 0.0251 AC: 88 AN: 3509

South Asian (SAS) AF: 0.0806 AC: 196 AN: 2432

European-Finnish (FIN) AF: 0.131 AC: 767 AN: 5854

Middle Eastern (MID) AF: 0.147 AC: 32 AN: 217

European-Non Finnish (NFE) AF: 0.159 AC: 8384 AN: 52621

Other (OTH) AF: 0.143 AC: 214 AN: 1497

Alfa AF: 0.154 Hom.: 3138

Bravo AF: 0.139

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.7
DANN	Benign	0.18
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs5938679; hg19: chrX-76003472;