X-121436975-T-G

Variant names:

• chrX-121436975-T-G
• rs1533901

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

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 0.80 (25061 hom., 26341 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0640
• Publications: 0 publications found

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).

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: 0.804 AC: 88566 AN: 110097 Hom.: 25058 Cov.: 22

Gnomad AFR AF: 0.793

Gnomad AMI AF: 0.901

Gnomad AMR AF: 0.873

Gnomad ASJ AF: 0.690

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.932

Gnomad FIN AF: 0.820

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.782

Gnomad OTH AF: 0.794

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

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.804 AC: 88617 AN: 110153 Hom.: 25061 Cov.: 22 AF XY: 0.812 AC XY: 26341 AN XY: 32427

African (AFR) AF: 0.793 AC: 24054 AN: 30319

American (AMR) AF: 0.873 AC: 9010 AN: 10320

Ashkenazi Jewish (ASJ) AF: 0.690 AC: 1817 AN: 2634

East Asian (EAS) AF: 0.999 AC: 3489 AN: 3492

South Asian (SAS) AF: 0.931 AC: 2392 AN: 2569

European-Finnish (FIN) AF: 0.820 AC: 4691 AN: 5718

Middle Eastern (MID) AF: 0.587 AC: 122 AN: 208

European-Non Finnish (NFE) AF: 0.782 AC: 41243 AN: 52723

Other (OTH) AF: 0.796 AC: 1189 AN: 1493

Alfa AF: 0.787 Hom.: 6587

Bravo AF: 0.809

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	10
DANN	Benign	0.68
PhyloP100		-0.064

Splicing

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

Other links and lift over

dbSNP: rs1533901; hg19: chrX-120570829;