X-140084524-C-T

Variant names:

• chrX-140084524-C-T
• rs5907577

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 0.246 in 111,201 control chromosomes in the GnomAD database, including 2,743 homozygotes. There are 8,283 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 0.25 (2743 hom., 8283 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.768
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.428 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.246 AC: 27365 AN: 111146 Hom.: 2747 Cov.: 23

Gnomad AFR AF: 0.0983

Gnomad AMI AF: 0.206

Gnomad AMR AF: 0.240

Gnomad ASJ AF: 0.392

Gnomad EAS AF: 0.210

Gnomad SAS AF: 0.452

Gnomad FIN AF: 0.321

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.310

Gnomad OTH AF: 0.250

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

GnomAD4 genome AF: 0.246 AC: 27350 AN: 111201 Hom.: 2743 Cov.: 23 AF XY: 0.248 AC XY: 8283 AN XY: 33431

African (AFR) AF: 0.0982 AC: 3020 AN: 30755

American (AMR) AF: 0.240 AC: 2521 AN: 10510

Ashkenazi Jewish (ASJ) AF: 0.392 AC: 1034 AN: 2635

East Asian (EAS) AF: 0.211 AC: 741 AN: 3516

South Asian (SAS) AF: 0.449 AC: 1170 AN: 2605

European-Finnish (FIN) AF: 0.321 AC: 1885 AN: 5868

Middle Eastern (MID) AF: 0.417 AC: 88 AN: 211

European-Non Finnish (NFE) AF: 0.310 AC: 16380 AN: 52921

Other (OTH) AF: 0.247 AC: 372 AN: 1506

Alfa AF: 0.215 Hom.: 4261

Bravo AF: 0.233

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.1
DANN	Benign	0.64
PhyloP100		0.77

Splicing

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

Other links and lift over

dbSNP: rs5907577; hg19: chrX-139166683;