rs1930218

Variant names:

• chrX-137153315-A-G
• rs1930218

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 0.201 in 111,152 control chromosomes in the GnomAD database, including 1,801 homozygotes. There are 6,625 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 0.20 (1801 hom., 6625 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.45

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.282 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: 0.201 AC: 22331 AN: 111098 Hom.: 1805 Cov.: 22 AF XY: 0.198 AC XY: 6616 AN XY: 33348

Gnomad AFR AF: 0.0997

Gnomad AMI AF: 0.354

Gnomad AMR AF: 0.282

Gnomad ASJ AF: 0.165

Gnomad EAS AF: 0.169

Gnomad SAS AF: 0.300

Gnomad FIN AF: 0.193

Gnomad MID AF: 0.273

Gnomad NFE AF: 0.241

Gnomad OTH AF: 0.224

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

GnomAD4 genome AF: 0.201 AC: 22335 AN: 111152 Hom.: 1801 Cov.: 22 AF XY: 0.198 AC XY: 6625 AN XY: 33412

Gnomad4 AFR AF: 0.0996

Gnomad4 AMR AF: 0.282

Gnomad4 ASJ AF: 0.165

Gnomad4 EAS AF: 0.170

Gnomad4 SAS AF: 0.299

Gnomad4 FIN AF: 0.193

Gnomad4 NFE AF: 0.241

Gnomad4 OTH AF: 0.228

Alfa AF: 0.207 Hom.: 1895

Bravo AF: 0.206

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	10
DANN	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1930218; hg19: chrX-136235474;