chrX-78328090-G-T

Variant names:

• chrX-78328090-G-T
• rs2637204

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 0.79 (24847 hom., 25011 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.84
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).

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: 0.789 AC: 86665 AN: 109903 Hom.: 24855 Cov.: 22

Gnomad AFR AF: 0.913

Gnomad AMI AF: 0.666

Gnomad AMR AF: 0.672

Gnomad ASJ AF: 0.814

Gnomad EAS AF: 0.592

Gnomad SAS AF: 0.620

Gnomad FIN AF: 0.772

Gnomad MID AF: 0.738

Gnomad NFE AF: 0.765

Gnomad OTH AF: 0.762

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: 0.789 AC: 86701 AN: 109956 Hom.: 24847 Cov.: 22 AF XY: 0.777 AC XY: 25011 AN XY: 32194

African (AFR) AF: 0.913 AC: 27569 AN: 30211

American (AMR) AF: 0.671 AC: 6916 AN: 10300

Ashkenazi Jewish (ASJ) AF: 0.814 AC: 2134 AN: 2622

East Asian (EAS) AF: 0.592 AC: 2043 AN: 3451

South Asian (SAS) AF: 0.617 AC: 1601 AN: 2594

European-Finnish (FIN) AF: 0.772 AC: 4370 AN: 5661

Middle Eastern (MID) AF: 0.759 AC: 164 AN: 216

European-Non Finnish (NFE) AF: 0.765 AC: 40338 AN: 52754

Other (OTH) AF: 0.758 AC: 1124 AN: 1483

Alfa AF: 0.776 Hom.: 23351

Bravo AF: 0.787

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.53
DANN	Benign	0.43
PhyloP100		-1.8
PromoterAI		0.0058	Neutral

Splicing

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

Other links and lift over

dbSNP: rs2637204; hg19: chrX-77583587;