rs3092920

Variant names:

• chrX-136661832-G-T
• rs3092920

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 0.225 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
• Publications: 10 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.225 AC: 25084 AN: 111496 Hom.: 3809 Cov.: 23

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

African (AFR) AF: 0.553 AC: 16897 AN: 30555

American (AMR) AF: 0.155 AC: 1640 AN: 10581

Ashkenazi Jewish (ASJ) AF: 0.138 AC: 365 AN: 2650

East Asian (EAS) AF: 0.103 AC: 368 AN: 3573

South Asian (SAS) AF: 0.230 AC: 619 AN: 2693

European-Finnish (FIN) AF: 0.0661 AC: 398 AN: 6017

Middle Eastern (MID) AF: 0.230 AC: 50 AN: 217

European-Non Finnish (NFE) AF: 0.0842 AC: 4468 AN: 53049

Other (OTH) AF: 0.208 AC: 318 AN: 1530

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
PhyloP100		-0.42

Splicing

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

Other links and lift over

dbSNP: rs3092920; hg19: chrX-135743991;