X-67801708-C-T

Variant names:

• chrX-67801708-C-T
• rs5919432

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 0.69 (19902 hom., 22728 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.111
• Publications: 52 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).

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: 0.693 AC: 76210 AN: 109912 Hom.: 19907 Cov.: 22

Gnomad AFR AF: 0.380

Gnomad AMI AF: 0.873

Gnomad AMR AF: 0.815

Gnomad ASJ AF: 0.801

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.904

Gnomad FIN AF: 0.822

Gnomad MID AF: 0.674

Gnomad NFE AF: 0.797

Gnomad OTH AF: 0.709

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: 0.693 AC: 76234 AN: 109964 Hom.: 19902 Cov.: 22 AF XY: 0.705 AC XY: 22728 AN XY: 32250

African (AFR) AF: 0.380 AC: 11496 AN: 30267

American (AMR) AF: 0.815 AC: 8379 AN: 10278

Ashkenazi Jewish (ASJ) AF: 0.801 AC: 2105 AN: 2629

East Asian (EAS) AF: 0.998 AC: 3466 AN: 3473

South Asian (SAS) AF: 0.905 AC: 2282 AN: 2521

European-Finnish (FIN) AF: 0.822 AC: 4695 AN: 5713

Middle Eastern (MID) AF: 0.654 AC: 138 AN: 211

European-Non Finnish (NFE) AF: 0.797 AC: 42016 AN: 52699

Other (OTH) AF: 0.713 AC: 1067 AN: 1497

Alfa AF: 0.757 Hom.: 82736

Bravo AF: 0.685

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.3
DANN	Benign	0.79
PhyloP100		-0.11

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs5919432;

hg19: chrX-67021550;