rs35352127

Variant names:

• chrX-858939-T-A
• rs35352127

Your query was ambiguous. Multiple possible variants found:

• chrX-858939-T-A
• chrX-858939-T-C
• chrX-858939-T-G

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 0.203 in 151,850 control chromosomes in the GnomAD database, including 3,406 homozygotes. There are 14,757 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 (3406 hom., 14757 hem., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.26

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.276 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: 0.203 AC: 30828 AN: 151732 Hom.: 3394 Cov.: 31 AF XY: 0.199 AC XY: 14710 AN XY: 74074

Gnomad AFR AF: 0.280

Gnomad AMI AF: 0.115

Gnomad AMR AF: 0.129

Gnomad ASJ AF: 0.126

Gnomad EAS AF: 0.208

Gnomad SAS AF: 0.209

Gnomad FIN AF: 0.141

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.188

Gnomad OTH AF: 0.176

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

GnomAD4 genome AF: 0.203 AC: 30877 AN: 151850 Hom.: 3406 Cov.: 31 AF XY: 0.199 AC XY: 14757 AN XY: 74202

Gnomad4 AFR AF: 0.281

Gnomad4 AMR AF: 0.128

Gnomad4 ASJ AF: 0.126

Gnomad4 EAS AF: 0.207

Gnomad4 SAS AF: 0.208

Gnomad4 FIN AF: 0.141

Gnomad4 NFE AF: 0.188

Gnomad4 OTH AF: 0.176

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.23
DANN	Benign	0.10

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs35352127; hg19: chrX-819674;