ENST00000630388.2:n.412-89960T>C

Variant names:

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

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000630388.2(MIR325HG):​n.412-89960T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 22)
• Consequence: MIR325HG ENST00000630388.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.55

Genes affected

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

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIR325HG	NR_110400.2	n.307-89960T>C		intron_variant	Intron 1 of 3
MIR325HG	NR_110401.2	n.412-124379T>C		intron_variant	Intron 2 of 3
MIR325HG	NR_110402.2	n.412-89960T>C		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR325HG	ENST00000630388.2	n.412-89960T>C		intron_variant	Intron 2 of 3	1
MIR325HG	ENST00000626742.1	n.382-89960T>C		intron_variant	Intron 2 of 3	4
MIR325HG	ENST00000626832.1	n.243-124379T>C		intron_variant	Intron 1 of 2	4

Frequencies

GnomAD3 genomes Cov.: 22

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

GnomAD4 genome Cov.: 22

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.8
DANN	Benign	0.76

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;