rs10521361

Variant names:

• chrX-82613452-A-C
• rs10521361

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.0185 in 112,230 control chromosomes in the GnomAD database, including 59 homozygotes. There are 632 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 0.019 (59 hom., 632 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.204
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0954 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: 0.0185 AC: 2075 AN: 112181 Hom.: 58 Cov.: 23

Gnomad AFR AF: 0.00243

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.100

Gnomad ASJ AF: 0.00677

Gnomad EAS AF: 0.0347

Gnomad SAS AF: 0.00330

Gnomad FIN AF: 0.0116

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0127

Gnomad OTH AF: 0.0301

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

GnomAD4 genome AF: 0.0185 AC: 2080 AN: 112230 Hom.: 59 Cov.: 23 AF XY: 0.0184 AC XY: 632 AN XY: 34390

African (AFR) AF: 0.00242 AC: 75 AN: 30979

American (AMR) AF: 0.100 AC: 1060 AN: 10556

Ashkenazi Jewish (ASJ) AF: 0.00677 AC: 18 AN: 2657

East Asian (EAS) AF: 0.0348 AC: 124 AN: 3559

South Asian (SAS) AF: 0.00331 AC: 9 AN: 2720

European-Finnish (FIN) AF: 0.0116 AC: 71 AN: 6100

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 218

European-Non Finnish (NFE) AF: 0.0127 AC: 678 AN: 53241

Other (OTH) AF: 0.0298 AC: 45 AN: 1512

Alfa AF: 0.0217 Hom.: 113

Bravo AF: 0.0274

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.63
DANN	Benign	0.75
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs10521361; hg19: chrX-81868901;