rs4844367

Variant names:

• chrX-69559027-G-A
• rs4844367

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 0.395 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.395 AC: 43920 AN: 111252 Hom.: 7426 Cov.: 23

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

African (AFR) AF: 0.114 AC: 3506 AN: 30861

American (AMR) AF: 0.561 AC: 5889 AN: 10489

Ashkenazi Jewish (ASJ) AF: 0.388 AC: 1025 AN: 2640

East Asian (EAS) AF: 0.699 AC: 2429 AN: 3474

South Asian (SAS) AF: 0.529 AC: 1389 AN: 2628

European-Finnish (FIN) AF: 0.513 AC: 3040 AN: 5921

Middle Eastern (MID) AF: 0.291 AC: 62 AN: 213

European-Non Finnish (NFE) AF: 0.484 AC: 25625 AN: 52895

Other (OTH) AF: 0.412 AC: 625 AN: 1517

Alfa AF: 0.459 Hom.: 42526

Bravo AF: 0.391

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.21
DANN	Benign	0.52
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs4844367; hg19: chrX-68778870;