chrX-83850275-C-T

Variant names:

• chrX-83850275-C-T
• rs1531868

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 0.111 in 110,924 control chromosomes in the GnomAD database, including 696 homozygotes. There are 3,594 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 0.11 (696 hom., 3594 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.193
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.477 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.111 AC: 12297 AN: 110871 Hom.: 699 Cov.: 22

Gnomad AFR AF: 0.0693

Gnomad AMI AF: 0.0929

Gnomad AMR AF: 0.0937

Gnomad ASJ AF: 0.127

Gnomad EAS AF: 0.496

Gnomad SAS AF: 0.246

Gnomad FIN AF: 0.109

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.0946

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

GnomAD4 genome AF: 0.111 AC: 12292 AN: 110924 Hom.: 696 Cov.: 22 AF XY: 0.108 AC XY: 3594 AN XY: 33152

African (AFR) AF: 0.0692 AC: 2116 AN: 30582

American (AMR) AF: 0.0936 AC: 980 AN: 10469

Ashkenazi Jewish (ASJ) AF: 0.127 AC: 334 AN: 2636

East Asian (EAS) AF: 0.496 AC: 1693 AN: 3410

South Asian (SAS) AF: 0.245 AC: 631 AN: 2580

European-Finnish (FIN) AF: 0.109 AC: 648 AN: 5965

Middle Eastern (MID) AF: 0.0558 AC: 12 AN: 215

European-Non Finnish (NFE) AF: 0.107 AC: 5672 AN: 52879

Other (OTH) AF: 0.0947 AC: 143 AN: 1510

Alfa AF: 0.121 Hom.: 2834

Bravo AF: 0.109

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.9
DANN	Benign	0.75
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs1531868; hg19: chrX-83105283;