rs5945680

Variant names:

• chrX-103336905-G-A
• rs5945680

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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 0.23 (2501 hom., 6012 hem., cov: 20)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.549
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.306 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.232 AC: 24409 AN: 105399 Hom.: 2503 Cov.: 20

Gnomad AFR AF: 0.146

Gnomad AMI AF: 0.152

Gnomad AMR AF: 0.162

Gnomad ASJ AF: 0.255

Gnomad EAS AF: 0.00930

Gnomad SAS AF: 0.194

Gnomad FIN AF: 0.214

Gnomad MID AF: 0.273

Gnomad NFE AF: 0.310

Gnomad OTH AF: 0.228

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

GnomAD4 genome AF: 0.231 AC: 24412 AN: 105452 Hom.: 2501 Cov.: 20 AF XY: 0.207 AC XY: 6012 AN XY: 29016

African (AFR) AF: 0.146 AC: 4210 AN: 28882

American (AMR) AF: 0.162 AC: 1575 AN: 9726

Ashkenazi Jewish (ASJ) AF: 0.255 AC: 649 AN: 2550

East Asian (EAS) AF: 0.00933 AC: 30 AN: 3216

South Asian (SAS) AF: 0.195 AC: 423 AN: 2166

European-Finnish (FIN) AF: 0.214 AC: 1091 AN: 5101

Middle Eastern (MID) AF: 0.271 AC: 57 AN: 210

European-Non Finnish (NFE) AF: 0.310 AC: 15955 AN: 51508

Other (OTH) AF: 0.225 AC: 321 AN: 1427

Alfa AF: 0.271 Hom.: 21409

Bravo AF: 0.221

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.81
DANN	Benign	0.70
PhyloP100		-0.55

Splicing

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

Other links and lift over

dbSNP: rs5945680; hg19: chrX-102591833;