rs1112491

chrX-42976072-A-G

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 0.223 in 111,338 control chromosomes in the GnomAD database, including 2,133 homozygotes. There are 7,127 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 0.22 (2133 hom., 7127 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.240

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.301 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.223 AC: 24801 AN: 111283 Hom.: 2134 Cov.: 23 AF XY: 0.213 AC XY: 7126 AN XY: 33489

Gnomad AFR AF: 0.230

Gnomad AMI AF: 0.359

Gnomad AMR AF: 0.129

Gnomad ASJ AF: 0.225

Gnomad EAS AF: 0.195

Gnomad SAS AF: 0.319

Gnomad FIN AF: 0.194

Gnomad MID AF: 0.179

Gnomad NFE AF: 0.236

Gnomad OTH AF: 0.206

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

GnomAD4 genome AF: 0.223 AC: 24800 AN: 111338 Hom.: 2133 Cov.: 23 AF XY: 0.212 AC XY: 7127 AN XY: 33554

Gnomad4 AFR AF: 0.230

Gnomad4 AMR AF: 0.129

Gnomad4 ASJ AF: 0.225

Gnomad4 EAS AF: 0.195

Gnomad4 SAS AF: 0.319

Gnomad4 FIN AF: 0.194

Gnomad4 NFE AF: 0.237

Gnomad4 OTH AF: 0.208

Alfa AF: 0.226 Hom.: 1028

Bravo AF: 0.215

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	4.4
Dann	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1112491; hg19: chrX-42835321;