rs5988437

Variant names:

• chrX-857097-C-G
• rs5988437

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 0.377 in 151,694 control chromosomes in the GnomAD database, including 12,918 homozygotes. There are 27,585 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 0.38 (12918 hom., 27585 hem., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.627 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.377 AC: 57099 AN: 151576 Hom.: 12887 Cov.: 31

Gnomad AFR AF: 0.633

Gnomad AMI AF: 0.304

Gnomad AMR AF: 0.333

Gnomad ASJ AF: 0.259

Gnomad EAS AF: 0.307

Gnomad SAS AF: 0.313

Gnomad FIN AF: 0.230

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.271

Gnomad OTH AF: 0.350

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

GnomAD4 genome AF: 0.377 AC: 57172 AN: 151694 Hom.: 12918 Cov.: 31 AF XY: 0.372 AC XY: 27585 AN XY: 74084

African (AFR) AF: 0.633 AC: 26187 AN: 41366

American (AMR) AF: 0.333 AC: 5072 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.259 AC: 898 AN: 3466

East Asian (EAS) AF: 0.307 AC: 1578 AN: 5136

South Asian (SAS) AF: 0.311 AC: 1491 AN: 4800

European-Finnish (FIN) AF: 0.230 AC: 2415 AN: 10518

Middle Eastern (MID) AF: 0.439 AC: 129 AN: 294

European-Non Finnish (NFE) AF: 0.271 AC: 18397 AN: 67884

Other (OTH) AF: 0.346 AC: 728 AN: 2102

Bravo AF: 0.395

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.18
DANN	Benign	0.27
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs5988437; hg19: chrX-817832;