X-890391-C-G

Variant names:

• chrX-890391-C-G
• rs5988459

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 0.4 in 152,020 control chromosomes in the GnomAD database, including 15,970 homozygotes. There are 30,275 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 0.40 (15970 hom., 30275 hem., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.60
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.746 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: 0.400 AC: 60755 AN: 151902 Hom.: 15934 Cov.: 32

Gnomad AFR AF: 0.703

Gnomad AMI AF: 0.421

Gnomad AMR AF: 0.385

Gnomad ASJ AF: 0.288

Gnomad EAS AF: 0.767

Gnomad SAS AF: 0.510

Gnomad FIN AF: 0.288

Gnomad MID AF: 0.344

Gnomad NFE AF: 0.207

Gnomad OTH AF: 0.364

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

GnomAD4 genome AF: 0.400 AC: 60841 AN: 152020 Hom.: 15970 Cov.: 32 AF XY: 0.408 AC XY: 30275 AN XY: 74270

African (AFR) AF: 0.704 AC: 29179 AN: 41472

American (AMR) AF: 0.385 AC: 5876 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.288 AC: 1000 AN: 3470

East Asian (EAS) AF: 0.766 AC: 3974 AN: 5186

South Asian (SAS) AF: 0.509 AC: 2449 AN: 4812

European-Finnish (FIN) AF: 0.288 AC: 3044 AN: 10566

Middle Eastern (MID) AF: 0.332 AC: 97 AN: 292

European-Non Finnish (NFE) AF: 0.207 AC: 14075 AN: 67926

Other (OTH) AF: 0.362 AC: 763 AN: 2110

Bravo AF: 0.424

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.95
DANN	Benign	0.46
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs5988459; hg19: chrX-851126;