rs1243792

Positions:

• chrX-41012314-G-A

Variant summary

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

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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.171

Genes affected

(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/exons	MANE	Protein	UniProt
		n.41012314G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000287549	ENST00000661498.1	n.143-3069C>T		intron_variant

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;