rs4468073

Positions:

• chrX-128983247-C-A
• chrX-128983247-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000653849.1(ENSG00000225689):​n.1435+49103G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.498 in 110,916 control chromosomes in the GnomAD database, including 11,487 homozygotes. There are 16,556 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 0.50 (11487 hom., 16556 hem., cov: 23)
• Consequence: ENSG00000225689 ENST00000653849.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.762

Genes affected

ENSG00000225689 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.667 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124905213	XR_007068316.1	n.5761+49103G>T		intron_variant
LOC124905213	XR_007068317.1	n.5702-14857G>T		intron_variant
LOC124905213	XR_007068319.1	n.5702-14857G>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000225689	ENST00000653849.1	n.1435+49103G>T		intron_variant
ENSG00000225689	ENST00000660383.1	n.567+49103G>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.498 AC: 55238 AN: 110861 Hom.: 11491 Cov.: 23 AF XY: 0.500 AC XY: 16541 AN XY: 33105

Gnomad AFR AF: 0.163

Gnomad AMI AF: 0.553

Gnomad AMR AF: 0.650

Gnomad ASJ AF: 0.576

Gnomad EAS AF: 0.690

Gnomad SAS AF: 0.691

Gnomad FIN AF: 0.575

Gnomad MID AF: 0.597

Gnomad NFE AF: 0.626

Gnomad OTH AF: 0.516

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

GnomAD4 genome AF: 0.498 AC: 55241 AN: 110916 Hom.: 11487 Cov.: 23 AF XY: 0.499 AC XY: 16556 AN XY: 33170

Gnomad4 AFR AF: 0.163

Gnomad4 AMR AF: 0.651

Gnomad4 ASJ AF: 0.576

Gnomad4 EAS AF: 0.690

Gnomad4 SAS AF: 0.691

Gnomad4 FIN AF: 0.575

Gnomad4 NFE AF: 0.626

Gnomad4 OTH AF: 0.520

Alfa AF: 0.548 Hom.: 4181

Bravo AF: 0.487

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.94
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4468073; hg19: chrX-128117224;