X-920268-A-G

Variant names:

• chrX-920268-A-G
• rs5988300

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 0.506 in 151,802 control chromosomes in the GnomAD database, including 20,093 homozygotes. There are 37,776 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 0.51 (20093 hom., 37776 hem., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.61
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.59).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.617 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.506 AC: 76786 AN: 151684 Hom.: 20063 Cov.: 31

Gnomad AFR AF: 0.623

Gnomad AMI AF: 0.509

Gnomad AMR AF: 0.522

Gnomad ASJ AF: 0.557

Gnomad EAS AF: 0.564

Gnomad SAS AF: 0.596

Gnomad FIN AF: 0.474

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.423

Gnomad OTH AF: 0.505

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

GnomAD4 genome AF: 0.506 AC: 76864 AN: 151802 Hom.: 20093 Cov.: 31 AF XY: 0.509 AC XY: 37776 AN XY: 74164

African (AFR) AF: 0.623 AC: 25786 AN: 41398

American (AMR) AF: 0.522 AC: 7962 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.557 AC: 1932 AN: 3466

East Asian (EAS) AF: 0.563 AC: 2903 AN: 5152

South Asian (SAS) AF: 0.597 AC: 2861 AN: 4796

European-Finnish (FIN) AF: 0.474 AC: 4985 AN: 10514

Middle Eastern (MID) AF: 0.537 AC: 158 AN: 294

European-Non Finnish (NFE) AF: 0.423 AC: 28763 AN: 67922

Other (OTH) AF: 0.499 AC: 1052 AN: 2110

Bravo AF: 0.513

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	3.7
DANN	Benign	0.27
PhyloP100		1.6

Splicing

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

Other links and lift over

dbSNP: rs5988300; hg19: chrX-881003;