chrX-147803630-C-A

Variant names:

• chrX-147803630-C-A
• rs5952066

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 0.23 in 110,632 control chromosomes in the GnomAD database, including 2,710 homozygotes. There are 7,089 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 0.23 (2710 hom., 7089 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.309
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.389 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

Frequencies

GnomAD3 genomes AF: 0.230 AC: 25405 AN: 110576 Hom.: 2709 Cov.: 23

Gnomad AFR AF: 0.395

Gnomad AMI AF: 0.0539

Gnomad AMR AF: 0.125

Gnomad ASJ AF: 0.164

Gnomad EAS AF: 0.00169

Gnomad SAS AF: 0.243

Gnomad FIN AF: 0.155

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.185

Gnomad OTH AF: 0.220

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

GnomAD4 genome AF: 0.230 AC: 25444 AN: 110632 Hom.: 2710 Cov.: 23 AF XY: 0.215 AC XY: 7089 AN XY: 32902

African (AFR) AF: 0.395 AC: 11957 AN: 30253

American (AMR) AF: 0.125 AC: 1302 AN: 10437

Ashkenazi Jewish (ASJ) AF: 0.164 AC: 432 AN: 2631

East Asian (EAS) AF: 0.00170 AC: 6 AN: 3538

South Asian (SAS) AF: 0.240 AC: 623 AN: 2595

European-Finnish (FIN) AF: 0.155 AC: 909 AN: 5848

Middle Eastern (MID) AF: 0.274 AC: 59 AN: 215

European-Non Finnish (NFE) AF: 0.185 AC: 9772 AN: 52910

Other (OTH) AF: 0.229 AC: 347 AN: 1518

Alfa AF: 0.207 Hom.: 13375

Bravo AF: 0.237

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.1
DANN	Benign	0.34
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs5952066; hg19: chrX-146885148;