rs5946541

Variant names:

• chrX-897556-T-C
• rs5946541

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 0.324 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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

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: 0.323 AC: 48911 AN: 151274 Hom.: 9539 Cov.: 30

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

African (AFR) AF: 0.488 AC: 20140 AN: 41244

American (AMR) AF: 0.283 AC: 4301 AN: 15206

Ashkenazi Jewish (ASJ) AF: 0.261 AC: 905 AN: 3466

East Asian (EAS) AF: 0.728 AC: 3705 AN: 5088

South Asian (SAS) AF: 0.492 AC: 2354 AN: 4786

European-Finnish (FIN) AF: 0.274 AC: 2866 AN: 10454

Middle Eastern (MID) AF: 0.269 AC: 78 AN: 290

European-Non Finnish (NFE) AF: 0.201 AC: 13628 AN: 67850

Other (OTH) AF: 0.298 AC: 623 AN: 2094

Bravo AF: 0.332

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.7
DANN	Benign	0.55
PhyloP100		-0.56

Splicing

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

Other links and lift over

dbSNP: rs5946541; hg19: chrX-858291;