rs5991601

Variant names:

• chrX-42831917-C-T
• rs5991601

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 0.0861 in 111,353 control chromosomes in the GnomAD database, including 399 homozygotes. There are 2,761 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 0.086 (399 hom., 2761 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.135

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.252 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: 0.0861 AC: 9586 AN: 111298 Hom.: 398 Cov.: 22 AF XY: 0.0822 AC XY: 2757 AN XY: 33522

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.00146

Gnomad AMR AF: 0.0602

Gnomad ASJ AF: 0.0580

Gnomad EAS AF: 0.266

Gnomad SAS AF: 0.142

Gnomad FIN AF: 0.0541

Gnomad MID AF: 0.0932

Gnomad NFE AF: 0.0599

Gnomad OTH AF: 0.0917

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

GnomAD4 genome AF: 0.0861 AC: 9586 AN: 111353 Hom.: 399 Cov.: 22 AF XY: 0.0822 AC XY: 2761 AN XY: 33587

Gnomad4 AFR AF: 0.125

Gnomad4 AMR AF: 0.0600

Gnomad4 ASJ AF: 0.0580

Gnomad4 EAS AF: 0.266

Gnomad4 SAS AF: 0.143

Gnomad4 FIN AF: 0.0541

Gnomad4 NFE AF: 0.0599

Gnomad4 OTH AF: 0.0911

Alfa AF: 0.0700 Hom.: 441

Bravo AF: 0.0916

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.0
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5991601; hg19: chrX-42691167;