rs4827155

Variant names:

• chrX-39449692-C-T
• rs4827155

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.444 AC: 48988 AN: 110314 Hom.: 8181 Cov.: 23

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

African (AFR) AF: 0.263 AC: 8019 AN: 30465

American (AMR) AF: 0.608 AC: 6331 AN: 10405

Ashkenazi Jewish (ASJ) AF: 0.553 AC: 1457 AN: 2635

East Asian (EAS) AF: 0.539 AC: 1867 AN: 3464

South Asian (SAS) AF: 0.545 AC: 1396 AN: 2563

European-Finnish (FIN) AF: 0.425 AC: 2449 AN: 5758

Middle Eastern (MID) AF: 0.502 AC: 108 AN: 215

European-Non Finnish (NFE) AF: 0.500 AC: 26366 AN: 52694

Other (OTH) AF: 0.469 AC: 706 AN: 1506

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
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs4827155; hg19: chrX-39308946;