rs5916687

Positions:

• chrX-4678097-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 0.2 in 111,263 control chromosomes in the GnomAD database, including 2,064 homozygotes. There are 6,320 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 (2064 hom., 6320 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.370

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.289 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.200 AC: 22247 AN: 111211 Hom.: 2065 Cov.: 23 AF XY: 0.189 AC XY: 6322 AN XY: 33467

Gnomad AFR AF: 0.0791

Gnomad AMI AF: 0.290

Gnomad AMR AF: 0.150

Gnomad ASJ AF: 0.310

Gnomad EAS AF: 0.00112

Gnomad SAS AF: 0.123

Gnomad FIN AF: 0.173

Gnomad MID AF: 0.261

Gnomad NFE AF: 0.293

Gnomad OTH AF: 0.215

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

GnomAD4 genome AF: 0.200 AC: 22235 AN: 111263 Hom.: 2064 Cov.: 23 AF XY: 0.188 AC XY: 6320 AN XY: 33529

Gnomad4 AFR AF: 0.0789

Gnomad4 AMR AF: 0.149

Gnomad4 ASJ AF: 0.310

Gnomad4 EAS AF: 0.00112

Gnomad4 SAS AF: 0.123

Gnomad4 FIN AF: 0.173

Gnomad4 NFE AF: 0.293

Gnomad4 OTH AF: 0.212

Alfa AF: 0.277 Hom.: 25647

Bravo AF: 0.194

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	2.6
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5916687; hg19: chrX-4596138;