rs1206229

chrX-137430976-G-A

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 0.0709 in 111,610 control chromosomes in the GnomAD database, including 361 homozygotes. There are 2,224 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 0.071 (361 hom., 2224 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.63

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.169 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0707 AC: 7890 AN: 111555 Hom.: 357 Cov.: 22 AF XY: 0.0656 AC XY: 2216 AN XY: 33769

Gnomad AFR AF: 0.173

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0331

Gnomad ASJ AF: 0.0969

Gnomad EAS AF: 0.130

Gnomad SAS AF: 0.0316

Gnomad FIN AF: 0.0140

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0244

Gnomad OTH AF: 0.0579

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

GnomAD4 genome AF: 0.0709 AC: 7910 AN: 111610 Hom.: 361 Cov.: 22 AF XY: 0.0657 AC XY: 2224 AN XY: 33834

Gnomad4 AFR AF: 0.173

Gnomad4 AMR AF: 0.0331

Gnomad4 ASJ AF: 0.0969

Gnomad4 EAS AF: 0.130

Gnomad4 SAS AF: 0.0317

Gnomad4 FIN AF: 0.0140

Gnomad4 NFE AF: 0.0244

Gnomad4 OTH AF: 0.0584

Alfa AF: 0.0506 Hom.: 260

Bravo AF: 0.0790

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.034
Dann	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1206229; hg19: chrX-136513135;