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).

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: 0.804 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 v4.3

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;