chrX-76850554-A-G

Variant names:

• chrX-76850554-A-G
• rs1118580
• ENST00000630388.2:n.411+156722T>C

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000630388.2(MIR325HG):​n.411+156722T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.85 (29336 hom., 27476 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: MIR325HG ENST00000630388.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.841
• Publications: 1 publications found

Genes affected

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

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).

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.307-157467T>C		intron	N/A
	MIR325HG	NR_110401.2		n.411+156722T>C		intron	N/A
	MIR325HG	NR_110402.2		n.411+156722T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR325HG	ENST00000630388.2	TSL:1	n.411+156722T>C		intron	N/A
	MIR325HG	ENST00000626742.1	TSL:4	n.381+156722T>C		intron	N/A
	MIR325HG	ENST00000626832.1	TSL:4	n.242+163673T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.850 AC: 93940 AN: 110454 Hom.: 29341 Cov.: 23

Gnomad AFR AF: 0.737

Gnomad AMI AF: 0.974

Gnomad AMR AF: 0.749

Gnomad ASJ AF: 0.953

Gnomad EAS AF: 0.238

Gnomad SAS AF: 0.751

Gnomad FIN AF: 0.923

Gnomad MID AF: 0.958

Gnomad NFE AF: 0.965

Gnomad OTH AF: 0.857

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

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.850 AC: 93990 AN: 110513 Hom.: 29336 Cov.: 23 AF XY: 0.839 AC XY: 27476 AN XY: 32731

African (AFR) AF: 0.737 AC: 22325 AN: 30285

American (AMR) AF: 0.749 AC: 7801 AN: 10417

Ashkenazi Jewish (ASJ) AF: 0.953 AC: 2518 AN: 2643

East Asian (EAS) AF: 0.238 AC: 824 AN: 3464

South Asian (SAS) AF: 0.753 AC: 1949 AN: 2587

European-Finnish (FIN) AF: 0.923 AC: 5347 AN: 5793

Middle Eastern (MID) AF: 0.958 AC: 206 AN: 215

European-Non Finnish (NFE) AF: 0.965 AC: 51054 AN: 52906

Other (OTH) AF: 0.856 AC: 1302 AN: 1521

Alfa AF: 0.783 Hom.: 2060

Bravo AF: 0.823

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.2
DANN	Benign	0.28
PhyloP100		-0.84

Splicing

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

Other links and lift over

dbSNP: rs1118580; hg19: chrX-76070979;