rs5945767

Variant names:

• chrX-103336515-T-C
• rs5945767

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 0.201 in 111,013 control chromosomes in the GnomAD database, including 2,253 homozygotes. There are 6,357 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 0.20 (2253 hom., 6357 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00500
• Publications: 1 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 (NFE) allele frequency at 95% confidence interval = 0.308 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: 0.201 AC: 22323 AN: 110962 Hom.: 2256 Cov.: 23

Gnomad AFR AF: 0.0403

Gnomad AMI AF: 0.146

Gnomad AMR AF: 0.156

Gnomad ASJ AF: 0.255

Gnomad EAS AF: 0.00588

Gnomad SAS AF: 0.182

Gnomad FIN AF: 0.239

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.311

Gnomad OTH AF: 0.209

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

GnomAD4 genome AF: 0.201 AC: 22320 AN: 111013 Hom.: 2253 Cov.: 23 AF XY: 0.191 AC XY: 6357 AN XY: 33263

African (AFR) AF: 0.0402 AC: 1236 AN: 30758

American (AMR) AF: 0.156 AC: 1628 AN: 10460

Ashkenazi Jewish (ASJ) AF: 0.255 AC: 670 AN: 2627

East Asian (EAS) AF: 0.00590 AC: 21 AN: 3561

South Asian (SAS) AF: 0.183 AC: 491 AN: 2676

European-Finnish (FIN) AF: 0.239 AC: 1388 AN: 5797

Middle Eastern (MID) AF: 0.233 AC: 50 AN: 215

European-Non Finnish (NFE) AF: 0.312 AC: 16422 AN: 52715

Other (OTH) AF: 0.207 AC: 315 AN: 1524

Alfa AF: 0.268 Hom.: 22806

Bravo AF: 0.184

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.3
DANN	Benign	0.83
PhyloP100		0.0050

Splicing

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

Other links and lift over

dbSNP: rs5945767; hg19: chrX-102591443;