rs2721997

chrX-51601840-C-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 0.0181 in 111,486 control chromosomes in the GnomAD database, including 20 homozygotes. There are 623 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 0.018 (20 hom., 623 hem., cov: 21)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0210

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0181 (2013/111486) while in subpopulation NFE AF= 0.0276 (1467/53071). AF 95% confidence interval is 0.0265. There are 20 homozygotes in gnomad4. There are 623 alleles in male gnomad4 subpopulation. Median coverage is 21. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 20 gene

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: 0.0181 AC: 2014 AN: 111437 Hom.: 20 Cov.: 21 AF XY: 0.0185 AC XY: 624 AN XY: 33651

Gnomad AFR AF: 0.00359

Gnomad AMI AF: 0.0552

Gnomad AMR AF: 0.0134

Gnomad ASJ AF: 0.00907

Gnomad EAS AF: 0.000282

Gnomad SAS AF: 0.0190

Gnomad FIN AF: 0.0228

Gnomad MID AF: 0.0672

Gnomad NFE AF: 0.0276

Gnomad OTH AF: 0.0213

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

GnomAD4 genome AF: 0.0181 AC: 2013 AN: 111486 Hom.: 20 Cov.: 21 AF XY: 0.0185 AC XY: 623 AN XY: 33710

Gnomad4 AFR AF: 0.00358

Gnomad4 AMR AF: 0.0134

Gnomad4 ASJ AF: 0.00907

Gnomad4 EAS AF: 0.000283

Gnomad4 SAS AF: 0.0187

Gnomad4 FIN AF: 0.0228

Gnomad4 NFE AF: 0.0276

Gnomad4 OTH AF: 0.0210

Alfa AF: 0.0248 Hom.: 324

Bravo AF: 0.0172

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	3.8
Dann	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2721997; hg19: chrX-51344692;