rs4827155

chrX-39449692-C-T

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 0.444 in 110,373 control chromosomes in the GnomAD database, including 8,184 homozygotes. There are 14,521 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 0.44 (8184 hom., 14521 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.411

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.596 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: 0.444 AC: 48988 AN: 110314 Hom.: 8181 Cov.: 23 AF XY: 0.445 AC XY: 14505 AN XY: 32570

Gnomad AFR AF: 0.263

Gnomad AMI AF: 0.461

Gnomad AMR AF: 0.608

Gnomad ASJ AF: 0.553

Gnomad EAS AF: 0.539

Gnomad SAS AF: 0.544

Gnomad FIN AF: 0.425

Gnomad MID AF: 0.496

Gnomad NFE AF: 0.500

Gnomad OTH AF: 0.465

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

GnomAD4 genome AF: 0.444 AC: 49007 AN: 110373 Hom.: 8184 Cov.: 23 AF XY: 0.445 AC XY: 14521 AN XY: 32639

Gnomad4 AFR AF: 0.263

Gnomad4 AMR AF: 0.608

Gnomad4 ASJ AF: 0.553

Gnomad4 EAS AF: 0.539

Gnomad4 SAS AF: 0.545

Gnomad4 FIN AF: 0.425

Gnomad4 NFE AF: 0.500

Gnomad4 OTH AF: 0.469

Alfa AF: 0.455 Hom.: 3230

Bravo AF: 0.451

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	1.7
Dann	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4827155; hg19: chrX-39308946;