rs5988437

chrX-857097-C-G

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 0.377 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.377 AC: 57099 AN: 151576 Hom.: 12887 Cov.: 31 AF XY: 0.372 AC XY: 27509 AN XY: 73956

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

Gnomad4 AFR AF: 0.633

Gnomad4 AMR AF: 0.333

Gnomad4 ASJ AF: 0.259

Gnomad4 EAS AF: 0.307

Gnomad4 SAS AF: 0.311

Gnomad4 FIN AF: 0.230

Gnomad4 NFE AF: 0.271

Gnomad4 OTH AF: 0.346

Bravo AF: 0.395

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	0.18
Dann	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5988437; hg19: chrX-817832;