rs3092948

Variant names:

• chrX-136645602-C-G
• rs3092948

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 0.271 in 110,868 control chromosomes in the GnomAD database, including 3,498 homozygotes. There are 8,896 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 0.27 (3498 hom., 8896 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.287
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.417 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: 0.271 AC: 30015 AN: 110815 Hom.: 3494 Cov.: 22

Gnomad AFR AF: 0.424

Gnomad AMI AF: 0.0555

Gnomad AMR AF: 0.413

Gnomad ASJ AF: 0.167

Gnomad EAS AF: 0.0847

Gnomad SAS AF: 0.335

Gnomad FIN AF: 0.191

Gnomad MID AF: 0.264

Gnomad NFE AF: 0.181

Gnomad OTH AF: 0.280

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

GnomAD4 genome AF: 0.271 AC: 30050 AN: 110868 Hom.: 3498 Cov.: 22 AF XY: 0.269 AC XY: 8896 AN XY: 33118

African (AFR) AF: 0.424 AC: 12881 AN: 30407

American (AMR) AF: 0.413 AC: 4303 AN: 10416

Ashkenazi Jewish (ASJ) AF: 0.167 AC: 442 AN: 2645

East Asian (EAS) AF: 0.0850 AC: 300 AN: 3530

South Asian (SAS) AF: 0.336 AC: 878 AN: 2615

European-Finnish (FIN) AF: 0.191 AC: 1122 AN: 5874

Middle Eastern (MID) AF: 0.276 AC: 59 AN: 214

European-Non Finnish (NFE) AF: 0.181 AC: 9596 AN: 52964

Other (OTH) AF: 0.284 AC: 431 AN: 1518

Alfa AF: 0.241 Hom.: 1472

Bravo AF: 0.298

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.67
DANN	Benign	0.63
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs3092948; hg19: chrX-135727761;