chrX-35047829-G-A

Variant names:

• chrX-35047829-G-A
• rs10522030

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 0.179 in 111,169 control chromosomes in the GnomAD database, including 1,299 homozygotes. There are 5,624 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 0.18 (1299 hom., 5624 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.288
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.214 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: 0.179 AC: 19895 AN: 111118 Hom.: 1300 Cov.: 22

Gnomad AFR AF: 0.218

Gnomad AMI AF: 0.189

Gnomad AMR AF: 0.139

Gnomad ASJ AF: 0.175

Gnomad EAS AF: 0.138

Gnomad SAS AF: 0.178

Gnomad FIN AF: 0.161

Gnomad MID AF: 0.132

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.153

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

GnomAD4 genome AF: 0.179 AC: 19906 AN: 111169 Hom.: 1299 Cov.: 22 AF XY: 0.168 AC XY: 5624 AN XY: 33423

African (AFR) AF: 0.218 AC: 6688 AN: 30641

American (AMR) AF: 0.139 AC: 1455 AN: 10466

Ashkenazi Jewish (ASJ) AF: 0.175 AC: 461 AN: 2630

East Asian (EAS) AF: 0.139 AC: 486 AN: 3501

South Asian (SAS) AF: 0.178 AC: 468 AN: 2634

European-Finnish (FIN) AF: 0.161 AC: 952 AN: 5919

Middle Eastern (MID) AF: 0.135 AC: 29 AN: 215

European-Non Finnish (NFE) AF: 0.170 AC: 9009 AN: 52965

Other (OTH) AF: 0.151 AC: 230 AN: 1519

Alfa AF: 0.137 Hom.: 1159

Bravo AF: 0.184

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.3
DANN	Benign	0.64
PhyloP100		0.29

Splicing

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

Other links and lift over

dbSNP: rs10522030; hg19: chrX-35065946;