rs4892718

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
MIR325HG	NR_110400.2	n.306+52068A>T		intron_variant	Intron 1 of 3
MIR325HG	NR_110401.2	n.411+45117A>T		intron_variant	Intron 2 of 3
MIR325HG	NR_110402.2	n.411+45117A>T		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>T		intron_variant	Intron 2 of 3	1
MIR325HG	ENST00000626742.1	n.381+45117A>T		intron_variant	Intron 2 of 3	4
MIR325HG	ENST00000626832.1	n.242+52068A>T		intron_variant	Intron 1 of 2	4

Frequencies

GnomAD3 genomes AF: 0.0000543 AC: 6 AN: 110596 Hom.: 0 Cov.: 23

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

African (AFR) AF: 0.00 AC: 0 AN: 30654

American (AMR) AF: 0.0000970 AC: 1 AN: 10313

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2628

East Asian (EAS) AF: 0.00 AC: 0 AN: 3531

South Asian (SAS) AF: 0.00 AC: 0 AN: 2594

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 5764

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 229

European-Non Finnish (NFE) AF: 0.0000949 AC: 5 AN: 52705

Other (OTH) AF: 0.00 AC: 0 AN: 1496

Alfa AF: 0.00 Hom.: 26352

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;