rs5946541

Positions:

• chrX-897556-T-C

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 0.324 in 151,388 control chromosomes in the GnomAD database, including 9,563 homozygotes. There are 24,481 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 0.32 (9563 hom., 24481 hem., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.558

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 (EAS) allele frequency at 95% confidence interval = 0.709 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.323 AC: 48911 AN: 151274 Hom.: 9539 Cov.: 30 AF XY: 0.331 AC XY: 24399 AN XY: 73770

Gnomad AFR AF: 0.488

Gnomad AMI AF: 0.419

Gnomad AMR AF: 0.283

Gnomad ASJ AF: 0.261

Gnomad EAS AF: 0.729

Gnomad SAS AF: 0.492

Gnomad FIN AF: 0.274

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.201

Gnomad OTH AF: 0.297

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

GnomAD4 genome AF: 0.324 AC: 48981 AN: 151388 Hom.: 9563 Cov.: 30 AF XY: 0.331 AC XY: 24481 AN XY: 73898

Gnomad4 AFR AF: 0.488

Gnomad4 AMR AF: 0.283

Gnomad4 ASJ AF: 0.261

Gnomad4 EAS AF: 0.728

Gnomad4 SAS AF: 0.492

Gnomad4 FIN AF: 0.274

Gnomad4 NFE AF: 0.201

Gnomad4 OTH AF: 0.298

Bravo AF: 0.332

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.7
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5946541; hg19: chrX-858291;