rs45631821

chrX-148166786-G-A

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;