rs1206229

Variant names:

• chrX-137430976-G-A
• rs1206229

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;