X-30310029-G-T

Variant names:

• chrX-30310029-G-T
• rs4829169

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 0.165 in 110,498 control chromosomes in the GnomAD database, including 1,166 homozygotes. There are 5,217 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 0.17 (1166 hom., 5217 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0680
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.194 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: 0.165 AC: 18274 AN: 110446 Hom.: 1165 Cov.: 23

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.239

Gnomad AMR AF: 0.110

Gnomad ASJ AF: 0.212

Gnomad EAS AF: 0.120

Gnomad SAS AF: 0.0845

Gnomad FIN AF: 0.250

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.197

Gnomad OTH AF: 0.144

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

GnomAD4 genome AF: 0.165 AC: 18282 AN: 110498 Hom.: 1166 Cov.: 23 AF XY: 0.159 AC XY: 5217 AN XY: 32754

African (AFR) AF: 0.121 AC: 3689 AN: 30432

American (AMR) AF: 0.110 AC: 1149 AN: 10448

Ashkenazi Jewish (ASJ) AF: 0.212 AC: 558 AN: 2630

East Asian (EAS) AF: 0.120 AC: 419 AN: 3498

South Asian (SAS) AF: 0.0852 AC: 216 AN: 2536

European-Finnish (FIN) AF: 0.250 AC: 1439 AN: 5758

Middle Eastern (MID) AF: 0.136 AC: 29 AN: 213

European-Non Finnish (NFE) AF: 0.197 AC: 10403 AN: 52794

Other (OTH) AF: 0.145 AC: 219 AN: 1515

Alfa AF: 0.180 Hom.: 7942

Bravo AF: 0.156

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.3
DANN	Benign	0.61
PhyloP100		0.068

Splicing

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

Other links and lift over

dbSNP: rs4829169; hg19: chrX-30328146;