rs1410530

Variant names:

• chrX-83280161-G-A
• rs1410530

Your query was ambiguous. Multiple possible variants found:

• chrX-83280161-G-A
• chrX-83280161-G-C
• chrX-83280161-G-T

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 0.196 in 110,614 control chromosomes in the GnomAD database, including 1,681 homozygotes. There are 6,295 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 0.20 (1681 hom., 6295 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.82
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.277 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.196 AC: 21651 AN: 110563 Hom.: 1681 Cov.: 22

Gnomad AFR AF: 0.280

Gnomad AMI AF: 0.0381

Gnomad AMR AF: 0.285

Gnomad ASJ AF: 0.107

Gnomad EAS AF: 0.173

Gnomad SAS AF: 0.139

Gnomad FIN AF: 0.172

Gnomad MID AF: 0.213

Gnomad NFE AF: 0.143

Gnomad OTH AF: 0.219

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

GnomAD4 genome AF: 0.196 AC: 21657 AN: 110614 Hom.: 1681 Cov.: 22 AF XY: 0.191 AC XY: 6295 AN XY: 32944

African (AFR) AF: 0.280 AC: 8514 AN: 30440

American (AMR) AF: 0.285 AC: 2953 AN: 10346

Ashkenazi Jewish (ASJ) AF: 0.107 AC: 280 AN: 2628

East Asian (EAS) AF: 0.173 AC: 600 AN: 3471

South Asian (SAS) AF: 0.140 AC: 369 AN: 2633

European-Finnish (FIN) AF: 0.172 AC: 1013 AN: 5896

Middle Eastern (MID) AF: 0.183 AC: 39 AN: 213

European-Non Finnish (NFE) AF: 0.143 AC: 7534 AN: 52804

Other (OTH) AF: 0.219 AC: 329 AN: 1500

Alfa AF: 0.170 Hom.: 4312

Bravo AF: 0.213

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.0010
DANN	Benign	0.20
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs1410530; hg19: chrX-82535169;