chrX-42976072-A-G

Variant names:

• chrX-42976072-A-G
• rs1112491

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.223 AC: 24801 AN: 111283 Hom.: 2134 Cov.: 23

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

African (AFR) AF: 0.230 AC: 7025 AN: 30579

American (AMR) AF: 0.129 AC: 1371 AN: 10596

Ashkenazi Jewish (ASJ) AF: 0.225 AC: 594 AN: 2641

East Asian (EAS) AF: 0.195 AC: 682 AN: 3504

South Asian (SAS) AF: 0.319 AC: 845 AN: 2651

European-Finnish (FIN) AF: 0.194 AC: 1171 AN: 6026

Middle Eastern (MID) AF: 0.160 AC: 34 AN: 213

European-Non Finnish (NFE) AF: 0.237 AC: 12518 AN: 52930

Other (OTH) AF: 0.208 AC: 317 AN: 1521

Alfa AF: 0.230 Hom.: 20343

Bravo AF: 0.215

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.4
DANN	Benign	0.76
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs1112491; hg19: chrX-42835321;