rs5945645

Positions:

• chrX-51569739-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0315 in 112,005 control chromosomes in the GnomAD database, including 72 homozygotes. There are 1,058 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 0.032 (72 hom., 1058 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.126

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0315 (3533/112005) while in subpopulation NFE AF= 0.0454 (2414/53203). AF 95% confidence interval is 0.0439. There are 72 homozygotes in gnomad4. There are 1058 alleles in male gnomad4 subpopulation. Median coverage is 23. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 72 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0315 AC: 3531 AN: 111950 Hom.: 72 Cov.: 23 AF XY: 0.0310 AC XY: 1056 AN XY: 34114

Gnomad AFR AF: 0.00597

Gnomad AMI AF: 0.225

Gnomad AMR AF: 0.0333

Gnomad ASJ AF: 0.0265

Gnomad EAS AF: 0.000281

Gnomad SAS AF: 0.0104

Gnomad FIN AF: 0.0446

Gnomad MID AF: 0.0169

Gnomad NFE AF: 0.0454

Gnomad OTH AF: 0.0378

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

GnomAD4 genome AF: 0.0315 AC: 3533 AN: 112005 Hom.: 72 Cov.: 23 AF XY: 0.0310 AC XY: 1058 AN XY: 34179

Gnomad4 AFR AF: 0.00595

Gnomad4 AMR AF: 0.0333

Gnomad4 ASJ AF: 0.0265

Gnomad4 EAS AF: 0.000282

Gnomad4 SAS AF: 0.0111

Gnomad4 FIN AF: 0.0446

Gnomad4 NFE AF: 0.0454

Gnomad4 OTH AF: 0.0373

Alfa AF: 0.0425 Hom.: 331

Bravo AF: 0.0315

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.074
DANN	Benign	0.14

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5945645; hg19: chrX-51312591;