rs5969181

Variant names:

• chrX-87368646-G-A
• rs5969181

Your query was ambiguous. Multiple possible variants found:

• chrX-87368646-G-A
• chrX-87368646-G-C

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 0.363 in 109,889 control chromosomes in the GnomAD database, including 5,355 homozygotes. There are 11,403 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 0.36 (5355 hom., 11403 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0580

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 (EAS) allele frequency at 95% confidence interval = 0.57 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: 0.363 AC: 39843 AN: 109842 Hom.: 5356 Cov.: 22 AF XY: 0.354 AC XY: 11395 AN XY: 32164

Gnomad AFR AF: 0.340

Gnomad AMI AF: 0.530

Gnomad AMR AF: 0.248

Gnomad ASJ AF: 0.311

Gnomad EAS AF: 0.591

Gnomad SAS AF: 0.309

Gnomad FIN AF: 0.385

Gnomad MID AF: 0.303

Gnomad NFE AF: 0.385

Gnomad OTH AF: 0.342

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

GnomAD4 genome AF: 0.363 AC: 39849 AN: 109889 Hom.: 5355 Cov.: 22 AF XY: 0.354 AC XY: 11403 AN XY: 32221

Gnomad4 AFR AF: 0.339

Gnomad4 AMR AF: 0.248

Gnomad4 ASJ AF: 0.311

Gnomad4 EAS AF: 0.592

Gnomad4 SAS AF: 0.310

Gnomad4 FIN AF: 0.385

Gnomad4 NFE AF: 0.385

Gnomad4 OTH AF: 0.344

Alfa AF: 0.358 Hom.: 20615

Bravo AF: 0.363

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.3
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5969181; hg19: chrX-86623649;