rs5979903

Variant names:

• chrX-13517290-C-T
• rs5979903

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.136 AC: 15123 AN: 110929 Hom.: 1453 Cov.: 22 AF XY: 0.124 AC XY: 4100 AN XY: 33161

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

Gnomad4 AFR AF: 0.346

Gnomad4 AMR AF: 0.0554

Gnomad4 ASJ AF: 0.0445

Gnomad4 EAS AF: 0.000842

Gnomad4 SAS AF: 0.0749

Gnomad4 FIN AF: 0.0639

Gnomad4 NFE AF: 0.0590

Gnomad4 OTH AF: 0.111

Alfa AF: 0.0776 Hom.: 3842

Bravo AF: 0.146

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5979903; hg19: chrX-13535409;