rs35841281

Variant names:

• chrX-859245-G-A
• rs35841281

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 0.0864 in 152,146 control chromosomes in the GnomAD database, including 760 homozygotes. There are 6,124 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 0.086 (760 hom., 6124 hem., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.171

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.134 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: 0.0865 AC: 13152 AN: 152028 Hom.: 760 Cov.: 32 AF XY: 0.0825 AC XY: 6123 AN XY: 74224

Gnomad AFR AF: 0.0220

Gnomad AMI AF: 0.0636

Gnomad AMR AF: 0.0743

Gnomad ASJ AF: 0.0894

Gnomad EAS AF: 0.0403

Gnomad SAS AF: 0.0371

Gnomad FIN AF: 0.0823

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.136

Gnomad OTH AF: 0.0893

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

GnomAD4 genome AF: 0.0864 AC: 13151 AN: 152146 Hom.: 760 Cov.: 32 AF XY: 0.0824 AC XY: 6124 AN XY: 74352

Gnomad4 AFR AF: 0.0219

Gnomad4 AMR AF: 0.0742

Gnomad4 ASJ AF: 0.0894

Gnomad4 EAS AF: 0.0404

Gnomad4 SAS AF: 0.0380

Gnomad4 FIN AF: 0.0823

Gnomad4 NFE AF: 0.136

Gnomad4 OTH AF: 0.0884

Bravo AF: 0.0844

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.1
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs35841281; hg19: chrX-819980;