rs1243792

Variant names:

• chrX-41012314-G-A
• rs1243792
• ENST00000661498.1:n.143-3069C>T

Variant summary

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

The ENST00000661498.1(ENSG00000287549):​n.143-3069C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.426 in 109,656 control chromosomes in the GnomAD database, including 7,314 homozygotes. There are 13,419 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 0.43 (7314 hom., 13419 hem., cov: 21)
• Consequence: ENSG00000287549 ENST00000661498.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.171

Genes affected

ENSG00000287549 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.523 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287549	ENST00000661498.1	n.143-3069C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.426 AC: 46719 AN: 109601 Hom.: 7324 Cov.: 21 AF XY: 0.420 AC XY: 13403 AN XY: 31949

Gnomad AFR AF: 0.343

Gnomad AMI AF: 0.402

Gnomad AMR AF: 0.400

Gnomad ASJ AF: 0.432

Gnomad EAS AF: 0.395

Gnomad SAS AF: 0.549

Gnomad FIN AF: 0.479

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.469

Gnomad OTH AF: 0.431

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

GnomAD4 genome AF: 0.426 AC: 46713 AN: 109656 Hom.: 7314 Cov.: 21 AF XY: 0.419 AC XY: 13419 AN XY: 32014

Gnomad4 AFR AF: 0.343

Gnomad4 AMR AF: 0.400

Gnomad4 ASJ AF: 0.432

Gnomad4 EAS AF: 0.395

Gnomad4 SAS AF: 0.547

Gnomad4 FIN AF: 0.479

Gnomad4 NFE AF: 0.469

Gnomad4 OTH AF: 0.430

Alfa AF: 0.465 Hom.: 43187

Bravo AF: 0.416

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	9.1
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1243792; hg19: chrX-40871567;