rs4892718

Positions:

• chrX-76962159-T-A
• chrX-76962159-T-G

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_Strong BS2

The ENST00000630388.2(MIR325HG):​n.411+45117A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000543 in 110,596 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 2 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 0.000054 (0 hom., 2 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 -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BS2: High Hemizygotes in GnomAd4 at 2 gene

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0000543 AC: 6 AN: 110596 Hom.: 0 Cov.: 23 AF XY: 0.0000609 AC XY: 2 AN XY: 32832

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0000970

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000949

Gnomad OTH AF: 0.00

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

GnomAD4 genome AF: 0.0000543 AC: 6 AN: 110596 Hom.: 0 Cov.: 23 AF XY: 0.0000609 AC XY: 2 AN XY: 32832

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.0000970

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000949

Gnomad4 OTH AF: 0.00

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;