chrX-100578978-T-C

Variant names:

• chrX-100578978-T-C
• rs873275

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 0.171 in 111,473 control chromosomes in the GnomAD database, including 1,456 homozygotes. There are 5,588 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 (1456 hom., 5588 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.213

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 (NFE) allele frequency at 95% confidence interval = 0.224 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: 0.171 AC: 19036 AN: 111421 Hom.: 1456 Cov.: 23 AF XY: 0.166 AC XY: 5578 AN XY: 33643

Gnomad AFR AF: 0.0676

Gnomad AMI AF: 0.259

Gnomad AMR AF: 0.190

Gnomad ASJ AF: 0.235

Gnomad EAS AF: 0.00280

Gnomad SAS AF: 0.126

Gnomad FIN AF: 0.257

Gnomad MID AF: 0.178

Gnomad NFE AF: 0.227

Gnomad OTH AF: 0.139

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

GnomAD4 genome AF: 0.171 AC: 19036 AN: 111473 Hom.: 1456 Cov.: 23 AF XY: 0.166 AC XY: 5588 AN XY: 33705

Gnomad4 AFR AF: 0.0677

Gnomad4 AMR AF: 0.189

Gnomad4 ASJ AF: 0.235

Gnomad4 EAS AF: 0.00281

Gnomad4 SAS AF: 0.127

Gnomad4 FIN AF: 0.257

Gnomad4 NFE AF: 0.227

Gnomad4 OTH AF: 0.138

Alfa AF: 0.212 Hom.: 5161

Bravo AF: 0.161

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.6
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs873275; hg19: chrX-99833975;