rs203648

Variant names:

• chrX-140538395-G-A
• rs203648

Your query was ambiguous. Multiple possible variants found:

• chrX-140538395-G-A
• chrX-140538395-G-C

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 0.349 in 110,811 control chromosomes in the GnomAD database, including 5,950 homozygotes. There are 11,256 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 0.35 (5950 hom., 11256 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0530

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) 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: 0.349 AC: 38690 AN: 110754 Hom.: 5950 Cov.: 22 AF XY: 0.341 AC XY: 11248 AN XY: 33000

Gnomad AFR AF: 0.0868

Gnomad AMI AF: 0.404

Gnomad AMR AF: 0.447

Gnomad ASJ AF: 0.453

Gnomad EAS AF: 0.568

Gnomad SAS AF: 0.381

Gnomad FIN AF: 0.344

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.459

Gnomad OTH AF: 0.389

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

GnomAD4 genome AF: 0.349 AC: 38690 AN: 110811 Hom.: 5950 Cov.: 22 AF XY: 0.340 AC XY: 11256 AN XY: 33067

Gnomad4 AFR AF: 0.0866

Gnomad4 AMR AF: 0.447

Gnomad4 ASJ AF: 0.453

Gnomad4 EAS AF: 0.567

Gnomad4 SAS AF: 0.383

Gnomad4 FIN AF: 0.344

Gnomad4 NFE AF: 0.459

Gnomad4 OTH AF: 0.393

Alfa AF: 0.380 Hom.: 2730

Bravo AF: 0.351

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.79
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs203648; hg19: chrX-139620560;