chrX-25551046-T-C

Variant names:

• chrX-25551046-T-C
• rs4129664
• ENST00000723704.1:n.470+73275T>C

Variant summary

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

The ENST00000723704.1(ENSG00000294456):​n.470+73275T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.12 in 111,592 control chromosomes in the GnomAD database, including 1,810 homozygotes. There are 3,588 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 0.12 (1810 hom., 3588 hem., cov: 22)
• Consequence: ENSG00000294456 ENST00000723704.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0800
• Publications: 0 publications found

Genes affected

ENSG00000294456 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.391 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000723704.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000294456	ENST00000723704.1		n.470+73275T>C		intron	N/A
	ENSG00000294456	ENST00000723705.1		n.521+73275T>C		intron	N/A
	ENSG00000294456	ENST00000723707.1		n.396+73275T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.120 AC: 13339 AN: 111541 Hom.: 1811 Cov.: 22

Gnomad AFR AF: 0.397

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0480

Gnomad ASJ AF: 0.0324

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00745

Gnomad FIN AF: 0.00211

Gnomad MID AF: 0.0546

Gnomad NFE AF: 0.00907

Gnomad OTH AF: 0.0965

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

GnomAD4 genome AF: 0.120 AC: 13355 AN: 111592 Hom.: 1810 Cov.: 22 AF XY: 0.106 AC XY: 3588 AN XY: 33834

African (AFR) AF: 0.397 AC: 12095 AN: 30443

American (AMR) AF: 0.0477 AC: 504 AN: 10565

Ashkenazi Jewish (ASJ) AF: 0.0324 AC: 86 AN: 2653

East Asian (EAS) AF: 0.00 AC: 0 AN: 3524

South Asian (SAS) AF: 0.00710 AC: 19 AN: 2676

European-Finnish (FIN) AF: 0.00211 AC: 13 AN: 6160

Middle Eastern (MID) AF: 0.0507 AC: 11 AN: 217

European-Non Finnish (NFE) AF: 0.00907 AC: 482 AN: 53145

Other (OTH) AF: 0.0953 AC: 145 AN: 1521

Alfa AF: 0.0614 Hom.: 1797

Bravo AF: 0.140

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.4
DANN	Benign	0.63
PhyloP100		0.080

Splicing

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

Other links and lift over

dbSNP: rs4129664; hg19: chrX-25569163;