X-79325907-T-C

Variant names:

• chrX-79325907-T-C
• rs1736653

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 0.90 (31673 hom., 27936 hem., cov: 21)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.956
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).

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: 0.902 AC: 97988 AN: 108579 Hom.: 31671 Cov.: 21

Gnomad AFR AF: 0.939

Gnomad AMI AF: 0.856

Gnomad AMR AF: 0.848

Gnomad ASJ AF: 0.924

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.969

Gnomad FIN AF: 0.882

Gnomad MID AF: 0.949

Gnomad NFE AF: 0.884

Gnomad OTH AF: 0.919

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: 0.903 AC: 98044 AN: 108632 Hom.: 31673 Cov.: 21 AF XY: 0.905 AC XY: 27936 AN XY: 30874

African (AFR) AF: 0.939 AC: 27934 AN: 29754

American (AMR) AF: 0.848 AC: 8678 AN: 10239

Ashkenazi Jewish (ASJ) AF: 0.924 AC: 2427 AN: 2626

East Asian (EAS) AF: 0.999 AC: 3429 AN: 3431

South Asian (SAS) AF: 0.971 AC: 2376 AN: 2446

European-Finnish (FIN) AF: 0.882 AC: 4805 AN: 5447

Middle Eastern (MID) AF: 0.949 AC: 204 AN: 215

European-Non Finnish (NFE) AF: 0.884 AC: 46272 AN: 52341

Other (OTH) AF: 0.920 AC: 1343 AN: 1460

Alfa AF: 0.901 Hom.: 9104

Bravo AF: 0.898

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.3
DANN	Benign	0.23
PhyloP100		-0.96

Splicing

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

Other links and lift over

dbSNP: rs1736653; hg19: chrX-78581404;