rs36208501

Variant names:

• chrX-860031-T-C
• rs36208501

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 0.061 (0 hom., 795 hem., cov: 0)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.83
• 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=-1.03).

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: 0.0611 AC: 1782 AN: 29188 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.0308

Gnomad AMI AF: 0.0565

Gnomad AMR AF: 0.0341

Gnomad ASJ AF: 0.0323

Gnomad EAS AF: 0.0345

Gnomad SAS AF: 0.129

Gnomad FIN AF: 0.0290

Gnomad MID AF: 0.0294

Gnomad NFE AF: 0.0811

Gnomad OTH AF: 0.0727

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: AS_VQSR AF: 0.0611 AC: 1783 AN: 29182 Hom.: 0 Cov.: 0 AF XY: 0.0589 AC XY: 795 AN XY: 13500

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.0308 AC: 204 AN: 6620

American (AMR) AF: 0.0341 AC: 86 AN: 2520

Ashkenazi Jewish (ASJ) AF: 0.0323 AC: 28 AN: 866

East Asian (EAS) AF: 0.0357 AC: 2 AN: 56

South Asian (SAS) AF: 0.131 AC: 38 AN: 290

European-Finnish (FIN) AF: 0.0290 AC: 50 AN: 1722

Middle Eastern (MID) AF: 0.0429 AC: 3 AN: 70

European-Non Finnish (NFE) AF: 0.0812 AC: 1329 AN: 16370

Other (OTH) AF: 0.0723 AC: 24 AN: 332

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.12
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs36208501; hg19: chrX-820766; COSMIC: COSV55181719;