rs3092945

Variant names:

• chrX-136647450-T-C
• rs3092945

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 0.0808 in 111,981 control chromosomes in the GnomAD database, including 837 homozygotes. There are 2,444 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 0.081 (837 hom., 2444 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.885
• Publications: 24 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.259 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: 0.0807 AC: 9030 AN: 111927 Hom.: 837 Cov.: 23

Gnomad AFR AF: 0.264

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0429

Gnomad ASJ AF: 0.0181

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00259

Gnomad FIN AF: 0.00163

Gnomad MID AF: 0.0844

Gnomad NFE AF: 0.00597

Gnomad OTH AF: 0.0666

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

GnomAD4 genome AF: 0.0808 AC: 9043 AN: 111981 Hom.: 837 Cov.: 23 AF XY: 0.0715 AC XY: 2444 AN XY: 34203

African (AFR) AF: 0.264 AC: 8084 AN: 30586

American (AMR) AF: 0.0428 AC: 456 AN: 10647

Ashkenazi Jewish (ASJ) AF: 0.0181 AC: 48 AN: 2645

East Asian (EAS) AF: 0.00 AC: 0 AN: 3585

South Asian (SAS) AF: 0.00260 AC: 7 AN: 2695

European-Finnish (FIN) AF: 0.00163 AC: 10 AN: 6139

Middle Eastern (MID) AF: 0.0926 AC: 20 AN: 216

European-Non Finnish (NFE) AF: 0.00597 AC: 318 AN: 53262

Other (OTH) AF: 0.0657 AC: 100 AN: 1521

Alfa AF: 0.0536 Hom.: 353

Bravo AF: 0.0933

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.64
DANN	Benign	0.62
PhyloP100		-0.89

Splicing

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

Other links and lift over

dbSNP: rs3092945; hg19: chrX-135729609;