rs10521550

Variant names:

• chrX-112576919-A-C
• rs10521550

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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 the male GnomAd4 subpopulation. Median coverage is 23. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 16 gene

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: 0.0129 AC: 1445 AN: 112086 Hom.: 16 Cov.: 23

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

African (AFR) AF: 0.00272 AC: 84 AN: 30933

American (AMR) AF: 0.0140 AC: 148 AN: 10594

Ashkenazi Jewish (ASJ) AF: 0.0136 AC: 36 AN: 2654

East Asian (EAS) AF: 0.00 AC: 0 AN: 3554

South Asian (SAS) AF: 0.0199 AC: 54 AN: 2708

European-Finnish (FIN) AF: 0.0119 AC: 72 AN: 6051

Middle Eastern (MID) AF: 0.0507 AC: 11 AN: 217

European-Non Finnish (NFE) AF: 0.0188 AC: 998 AN: 53209

Other (OTH) AF: 0.0163 AC: 25 AN: 1531

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
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs10521550; hg19: chrX-111820147;