rs5979903

Variant names:

• chrX-13517290-C-T
• rs5979903

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 0.136 in 110,979 control chromosomes in the GnomAD database, including 1,455 homozygotes. There are 4,114 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 0.14 (1455 hom., 4114 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.473
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.34 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: 0.136 AC: 15123 AN: 110929 Hom.: 1453 Cov.: 22

Gnomad AFR AF: 0.346

Gnomad AMI AF: 0.0916

Gnomad AMR AF: 0.0554

Gnomad ASJ AF: 0.0445

Gnomad EAS AF: 0.000840

Gnomad SAS AF: 0.0747

Gnomad FIN AF: 0.0639

Gnomad MID AF: 0.0940

Gnomad NFE AF: 0.0590

Gnomad OTH AF: 0.113

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

GnomAD4 genome AF: 0.136 AC: 15142 AN: 110979 Hom.: 1455 Cov.: 22 AF XY: 0.124 AC XY: 4114 AN XY: 33221

African (AFR) AF: 0.346 AC: 10488 AN: 30309

American (AMR) AF: 0.0554 AC: 582 AN: 10513

Ashkenazi Jewish (ASJ) AF: 0.0445 AC: 117 AN: 2628

East Asian (EAS) AF: 0.000842 AC: 3 AN: 3561

South Asian (SAS) AF: 0.0749 AC: 195 AN: 2604

European-Finnish (FIN) AF: 0.0639 AC: 384 AN: 6012

Middle Eastern (MID) AF: 0.0939 AC: 20 AN: 213

European-Non Finnish (NFE) AF: 0.0590 AC: 3122 AN: 52945

Other (OTH) AF: 0.111 AC: 169 AN: 1517

Alfa AF: 0.0913 Hom.: 6608

Bravo AF: 0.146

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.52
DANN	Benign	0.39
PhyloP100		-0.47

Splicing

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

Other links and lift over

dbSNP: rs5979903; hg19: chrX-13535409;