rs45631821

Variant names:

• chrX-148166786-G-A
• rs45631821

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.0779 in 110,622 control chromosomes in the GnomAD database, including 271 homozygotes. There are 2,429 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 0.078 (271 hom., 2429 hem., cov: 21)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00300

ACMG classification

Verdict is Benign. Variant got -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 = 0.0915 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: 0.0778 AC: 8605 AN: 110578 Hom.: 271 Cov.: 21 AF XY: 0.0737 AC XY: 2419 AN XY: 32840

Gnomad AFR AF: 0.0727

Gnomad AMI AF: 0.0119

Gnomad AMR AF: 0.0582

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.00114

Gnomad SAS AF: 0.0162

Gnomad FIN AF: 0.0572

Gnomad MID AF: 0.0936

Gnomad NFE AF: 0.0937

Gnomad OTH AF: 0.0976

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

GnomAD4 genome AF: 0.0779 AC: 8615 AN: 110622 Hom.: 271 Cov.: 21 AF XY: 0.0738 AC XY: 2429 AN XY: 32894

Gnomad4 AFR AF: 0.0730

Gnomad4 AMR AF: 0.0582

Gnomad4 ASJ AF: 0.108

Gnomad4 EAS AF: 0.00114

Gnomad4 SAS AF: 0.0163

Gnomad4 FIN AF: 0.0572

Gnomad4 NFE AF: 0.0937

Gnomad4 OTH AF: 0.0971

Alfa AF: 0.0813 Hom.: 467

Bravo AF: 0.0790

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.18
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs45631821; hg19: chrX-147248306;