rs734329

Positions:

• chrX-42754100-A-C
• chrX-42754100-A-T

Variant summary

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

The ENST00000671190.1(ENSG00000287223):​n.183+1610T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.322 in 108,489 control chromosomes in the GnomAD database, including 6,131 homozygotes. There are 9,446 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 0.32 (6131 hom., 9446 hem., cov: 21)
• Consequence: ENSG00000287223 ENST00000671190.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.58

Genes affected

ENSG00000287223 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.709 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105373186	XR_002958821.2	n.210+1610T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000287223	ENST00000671190.1	n.183+1610T>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.321 AC: 34822 AN: 108443 Hom.: 6125 Cov.: 21 AF XY: 0.305 AC XY: 9398 AN XY: 30845

Gnomad AFR AF: 0.614

Gnomad AMI AF: 0.310

Gnomad AMR AF: 0.428

Gnomad ASJ AF: 0.138

Gnomad EAS AF: 0.734

Gnomad SAS AF: 0.222

Gnomad FIN AF: 0.174

Gnomad MID AF: 0.0819

Gnomad NFE AF: 0.140

Gnomad OTH AF: 0.315

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

GnomAD4 genome AF: 0.322 AC: 34886 AN: 108489 Hom.: 6131 Cov.: 21 AF XY: 0.306 AC XY: 9446 AN XY: 30901

Gnomad4 AFR AF: 0.615

Gnomad4 AMR AF: 0.429

Gnomad4 ASJ AF: 0.138

Gnomad4 EAS AF: 0.733

Gnomad4 SAS AF: 0.219

Gnomad4 FIN AF: 0.174

Gnomad4 NFE AF: 0.140

Gnomad4 OTH AF: 0.316

Alfa AF: 0.181 Hom.: 6616

Bravo AF: 0.369

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.12
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs734329; hg19: chrX-42613351;