X-877619-C-G

Variant names:

• chrX-877619-C-G
• rs5946526

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 0.317 in 151,980 control chromosomes in the GnomAD database, including 8,089 homozygotes. There are 23,705 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 (8089 hom., 23705 hem., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.325
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.419 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.316 AC: 48054 AN: 151862 Hom.: 8066 Cov.: 32

Gnomad AFR AF: 0.424

Gnomad AMI AF: 0.427

Gnomad AMR AF: 0.324

Gnomad ASJ AF: 0.237

Gnomad EAS AF: 0.164

Gnomad SAS AF: 0.231

Gnomad FIN AF: 0.337

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.267

Gnomad OTH AF: 0.315

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

GnomAD4 genome AF: 0.317 AC: 48117 AN: 151980 Hom.: 8089 Cov.: 32 AF XY: 0.319 AC XY: 23705 AN XY: 74258

African (AFR) AF: 0.424 AC: 17569 AN: 41436

American (AMR) AF: 0.325 AC: 4958 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.237 AC: 822 AN: 3472

East Asian (EAS) AF: 0.164 AC: 848 AN: 5180

South Asian (SAS) AF: 0.231 AC: 1113 AN: 4810

European-Finnish (FIN) AF: 0.337 AC: 3562 AN: 10562

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.267 AC: 18117 AN: 67944

Other (OTH) AF: 0.311 AC: 657 AN: 2112

Bravo AF: 0.320

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.81
DANN	Benign	0.54
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs5946526; hg19: chrX-838354;