rs1118580

chrX-76850554-A-GchrX-76850554-A-T

Variant summary

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

The NR_110404.2(MIR325HG):n.306+163673T>C variant causes a intron, non coding transcript 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 NR_110404.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.841

Genes affected

MIR325HG (HGNC:):

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BS2: High Homozygotes in GnomAd at 29341 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MIR325HG	NR_110404.2	n.306+163673T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIR325HG	ENST00000658368.1	n.379+156722T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.850 AC: 93940 AN: 110454 Hom.: 29341 Cov.: 23 AF XY: 0.839 AC XY: 27417 AN XY: 32664

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

Gnomad4 AFR AF: 0.737

Gnomad4 AMR AF: 0.749

Gnomad4 ASJ AF: 0.953

Gnomad4 EAS AF: 0.238

Gnomad4 SAS AF: 0.753

Gnomad4 FIN AF: 0.923

Gnomad4 NFE AF: 0.965

Gnomad4 OTH AF: 0.856

Alfa AF: 0.783 Hom.: 2060

Bravo AF: 0.823

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	2.2
Dann	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1118580; hg19: chrX-76070979;