rs10521550

Positions:

• chrX-112576919-A-C

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 0.0129 in 112,137 control chromosomes in the GnomAD database, including 16 homozygotes. There are 416 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 0.013 (16 hom., 416 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.143

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BS1: Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.0129 (1449/112137) while in subpopulation SAS AF= 0.0199 (54/2708). AF 95% confidence interval is 0.0178. There are 16 homozygotes in gnomad4. There are 416 alleles in male gnomad4 subpopulation. Median coverage is 23. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 16 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: 0.0129 AC: 1445 AN: 112086 Hom.: 16 Cov.: 23 AF XY: 0.0120 AC XY: 412 AN XY: 34250

Gnomad AFR AF: 0.00269

Gnomad AMI AF: 0.0306

Gnomad AMR AF: 0.0140

Gnomad ASJ AF: 0.0136

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0191

Gnomad FIN AF: 0.0119

Gnomad MID AF: 0.0462

Gnomad NFE AF: 0.0188

Gnomad OTH AF: 0.0159

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

GnomAD4 genome AF: 0.0129 AC: 1449 AN: 112137 Hom.: 16 Cov.: 23 AF XY: 0.0121 AC XY: 416 AN XY: 34311

Gnomad4 AFR AF: 0.00272

Gnomad4 AMR AF: 0.0140

Gnomad4 ASJ AF: 0.0136

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.0199

Gnomad4 FIN AF: 0.0119

Gnomad4 NFE AF: 0.0188

Gnomad4 OTH AF: 0.0163

Alfa AF: 0.0154 Hom.: 89

Bravo AF: 0.0126

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.2
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10521550; hg19: chrX-111820147;