rs5916687

Variant names:

• chrX-4678097-G-A
• rs5916687

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;