rs4844367

Variant names:

• chrX-69559027-G-A
• rs4844367

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 0.395 in 111,306 control chromosomes in the GnomAD database, including 7,433 homozygotes. There are 13,368 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 0.39 (7433 hom., 13368 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.320

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.676 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: 0.395 AC: 43920 AN: 111252 Hom.: 7426 Cov.: 23 AF XY: 0.399 AC XY: 13346 AN XY: 33478

Gnomad AFR AF: 0.113

Gnomad AMI AF: 0.531

Gnomad AMR AF: 0.561

Gnomad ASJ AF: 0.388

Gnomad EAS AF: 0.699

Gnomad SAS AF: 0.529

Gnomad FIN AF: 0.513

Gnomad MID AF: 0.286

Gnomad NFE AF: 0.484

Gnomad OTH AF: 0.405

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

GnomAD4 genome AF: 0.395 AC: 43945 AN: 111306 Hom.: 7433 Cov.: 23 AF XY: 0.399 AC XY: 13368 AN XY: 33542

Gnomad4 AFR AF: 0.114

Gnomad4 AMR AF: 0.561

Gnomad4 ASJ AF: 0.388

Gnomad4 EAS AF: 0.699

Gnomad4 SAS AF: 0.529

Gnomad4 FIN AF: 0.513

Gnomad4 NFE AF: 0.484

Gnomad4 OTH AF: 0.412

Alfa AF: 0.474 Hom.: 30816

Bravo AF: 0.391

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.21
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4844367; hg19: chrX-68778870;