rs1029496

Positions:

• chrX-24379974-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 0.122 in 112,614 control chromosomes in the GnomAD database, including 649 homozygotes. There are 4,390 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 0.12 (649 hom., 4390 hem., cov: 24)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.513

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.241 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: 0.122 AC: 13695 AN: 112559 Hom.: 648 Cov.: 24 AF XY: 0.126 AC XY: 4386 AN XY: 34719

Gnomad AFR AF: 0.0659

Gnomad AMI AF: 0.0392

Gnomad AMR AF: 0.162

Gnomad ASJ AF: 0.0976

Gnomad EAS AF: 0.141

Gnomad SAS AF: 0.258

Gnomad FIN AF: 0.207

Gnomad MID AF: 0.126

Gnomad NFE AF: 0.130

Gnomad OTH AF: 0.126

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

GnomAD4 genome AF: 0.122 AC: 13696 AN: 112614 Hom.: 649 Cov.: 24 AF XY: 0.126 AC XY: 4390 AN XY: 34784

Gnomad4 AFR AF: 0.0659

Gnomad4 AMR AF: 0.162

Gnomad4 ASJ AF: 0.0976

Gnomad4 EAS AF: 0.141

Gnomad4 SAS AF: 0.257

Gnomad4 FIN AF: 0.207

Gnomad4 NFE AF: 0.130

Gnomad4 OTH AF: 0.127

Alfa AF: 0.123 Hom.: 906

Bravo AF: 0.121

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.34
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1029496; hg19: chrX-24398091;