chrX-11687501-A-C

Variant names:

• chrX-11687501-A-C
• rs7882574
• ENST00000634846.1:n.1104-18311T>G

Variant summary

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

The ENST00000634846.1(ENSG00000282840):​n.1104-18311T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.164 in 109,012 control chromosomes in the GnomAD database, including 1,895 homozygotes. There are 4,889 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 0.16 (1895 hom., 4889 hem., cov: 21)
• Consequence: ENSG00000282840 ENST00000634846.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.02

Genes affected

ENSG00000282840 (HGNC:56856): (MSL3 divergent transcript)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.358 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
ENSG00000282840	ENST00000634846.1	n.1104-18311T>G		intron_variant	Intron 3 of 3	5

Frequencies

GnomAD3 genomes AF: 0.164 AC: 17860 AN: 108959 Hom.: 1887 Cov.: 21 AF XY: 0.155 AC XY: 4853 AN XY: 31367

Gnomad AFR AF: 0.363

Gnomad AMI AF: 0.0147

Gnomad AMR AF: 0.233

Gnomad ASJ AF: 0.0962

Gnomad EAS AF: 0.232

Gnomad SAS AF: 0.0823

Gnomad FIN AF: 0.0544

Gnomad MID AF: 0.0944

Gnomad NFE AF: 0.0550

Gnomad OTH AF: 0.157

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

GnomAD4 genome AF: 0.164 AC: 17912 AN: 109012 Hom.: 1895 Cov.: 21 AF XY: 0.156 AC XY: 4889 AN XY: 31430

Gnomad4 AFR AF: 0.364

Gnomad4 AMR AF: 0.233

Gnomad4 ASJ AF: 0.0962

Gnomad4 EAS AF: 0.233

Gnomad4 SAS AF: 0.0826

Gnomad4 FIN AF: 0.0544

Gnomad4 NFE AF: 0.0549

Gnomad4 OTH AF: 0.156

Alfa AF: 0.0891 Hom.: 3082

Bravo AF: 0.193

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.7
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7882574; hg19: chrX-11705621;