rs3092920

chrX-136661832-G-T

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 0.225 in 111,550 control chromosomes in the GnomAD database, including 3,814 homozygotes. There are 7,266 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 (3814 hom., 7266 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.419

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.546 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: 0.225 AC: 25084 AN: 111496 Hom.: 3809 Cov.: 23 AF XY: 0.214 AC XY: 7236 AN XY: 33766

Gnomad AFR AF: 0.553

Gnomad AMI AF: 0.00292

Gnomad AMR AF: 0.155

Gnomad ASJ AF: 0.138

Gnomad EAS AF: 0.103

Gnomad SAS AF: 0.229

Gnomad FIN AF: 0.0661

Gnomad MID AF: 0.223

Gnomad NFE AF: 0.0842

Gnomad OTH AF: 0.203

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

GnomAD4 genome AF: 0.225 AC: 25125 AN: 111550 Hom.: 3814 Cov.: 23 AF XY: 0.215 AC XY: 7266 AN XY: 33830

Gnomad4 AFR AF: 0.553

Gnomad4 AMR AF: 0.155

Gnomad4 ASJ AF: 0.138

Gnomad4 EAS AF: 0.103

Gnomad4 SAS AF: 0.230

Gnomad4 FIN AF: 0.0661

Gnomad4 NFE AF: 0.0842

Gnomad4 OTH AF: 0.208

Alfa AF: 0.222 Hom.: 2119

Bravo AF: 0.247

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.20
Dann	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3092920; hg19: chrX-135743991;