chrX-76962159-T-G

Variant names:

• chrX-76962159-T-G
• rs4892718
• ENST00000630388.2:n.411+45117A>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000630388.2(MIR325HG):​n.411+45117A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.601 in 110,603 control chromosomes in the GnomAD database, including 17,555 homozygotes. There are 19,632 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 0.60 (17555 hom., 19632 hem., cov: 23)
• Consequence: MIR325HG ENST00000630388.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.312
• 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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.821 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIR325HG	NR_110400.2	n.306+52068A>C		intron_variant	Intron 1 of 3
MIR325HG	NR_110401.2	n.411+45117A>C		intron_variant	Intron 2 of 3
MIR325HG	NR_110402.2	n.411+45117A>C		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR325HG	ENST00000630388.2	n.411+45117A>C		intron_variant	Intron 2 of 3	1
MIR325HG	ENST00000626742.1	n.381+45117A>C		intron_variant	Intron 2 of 3	4
MIR325HG	ENST00000626832.1	n.242+52068A>C		intron_variant	Intron 1 of 2	4

Frequencies

GnomAD3 genomes AF: 0.602 AC: 66514 AN: 110552 Hom.: 17568 Cov.: 23

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.927

Gnomad AMR AF: 0.613

Gnomad ASJ AF: 0.811

Gnomad EAS AF: 0.209

Gnomad SAS AF: 0.654

Gnomad FIN AF: 0.832

Gnomad MID AF: 0.773

Gnomad NFE AF: 0.828

Gnomad OTH AF: 0.639

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

GnomAD4 genome AF: 0.601 AC: 66513 AN: 110603 Hom.: 17555 Cov.: 23 AF XY: 0.597 AC XY: 19632 AN XY: 32871

African (AFR) AF: 0.178 AC: 5453 AN: 30712

American (AMR) AF: 0.614 AC: 6336 AN: 10321

Ashkenazi Jewish (ASJ) AF: 0.811 AC: 2131 AN: 2628

East Asian (EAS) AF: 0.209 AC: 733 AN: 3513

South Asian (SAS) AF: 0.657 AC: 1698 AN: 2585

European-Finnish (FIN) AF: 0.832 AC: 4792 AN: 5758

Middle Eastern (MID) AF: 0.766 AC: 160 AN: 209

European-Non Finnish (NFE) AF: 0.828 AC: 43618 AN: 52682

Other (OTH) AF: 0.635 AC: 960 AN: 1513

Alfa AF: 0.702 Hom.: 26352

Bravo AF: 0.563

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
PhyloP100		-0.31

Splicing

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

Other links and lift over

dbSNP: rs4892718; hg19: chrX-76182584;