rs5905779

chrX-49872019-C-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 0.236 in 111,181 control chromosomes in the GnomAD database, including 3,067 homozygotes. There are 7,404 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 0.24 (3067 hom., 7404 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.245

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.429 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.236 AC: 26207 AN: 111127 Hom.: 3061 Cov.: 23 AF XY: 0.221 AC XY: 7367 AN XY: 33379

Gnomad AFR AF: 0.435

Gnomad AMI AF: 0.244

Gnomad AMR AF: 0.303

Gnomad ASJ AF: 0.227

Gnomad EAS AF: 0.0512

Gnomad SAS AF: 0.0657

Gnomad FIN AF: 0.0705

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.149

Gnomad OTH AF: 0.223

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

GnomAD4 genome AF: 0.236 AC: 26254 AN: 111181 Hom.: 3067 Cov.: 23 AF XY: 0.221 AC XY: 7404 AN XY: 33443

Gnomad4 AFR AF: 0.436

Gnomad4 AMR AF: 0.303

Gnomad4 ASJ AF: 0.227

Gnomad4 EAS AF: 0.0510

Gnomad4 SAS AF: 0.0656

Gnomad4 FIN AF: 0.0705

Gnomad4 NFE AF: 0.149

Gnomad4 OTH AF: 0.222

Alfa AF: 0.190 Hom.: 1283

Bravo AF: 0.269

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	0.40
Dann	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5905779; hg19: chrX-49636622;