X-117540100-T-C

Variant names:

• chrX-117540100-T-C
• rs736818

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 0.70 (19970 hom., 22754 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.390
• 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=-0.93).

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.697 AC: 76597 AN: 109917 Hom.: 19963 Cov.: 22

Gnomad AFR AF: 0.925

Gnomad AMI AF: 0.403

Gnomad AMR AF: 0.771

Gnomad ASJ AF: 0.600

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.868

Gnomad FIN AF: 0.569

Gnomad MID AF: 0.654

Gnomad NFE AF: 0.546

Gnomad OTH AF: 0.684

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: 0.697 AC: 76663 AN: 109968 Hom.: 19970 Cov.: 22 AF XY: 0.705 AC XY: 22754 AN XY: 32268

African (AFR) AF: 0.925 AC: 28044 AN: 30303

American (AMR) AF: 0.772 AC: 7984 AN: 10348

Ashkenazi Jewish (ASJ) AF: 0.600 AC: 1577 AN: 2630

East Asian (EAS) AF: 0.999 AC: 3437 AN: 3442

South Asian (SAS) AF: 0.867 AC: 2211 AN: 2551

European-Finnish (FIN) AF: 0.569 AC: 3261 AN: 5732

Middle Eastern (MID) AF: 0.671 AC: 141 AN: 210

European-Non Finnish (NFE) AF: 0.546 AC: 28711 AN: 52591

Other (OTH) AF: 0.689 AC: 1027 AN: 1491

Alfa AF: 0.623 Hom.: 14327

Bravo AF: 0.723

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.95
DANN	Benign	0.66
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs736818; hg19: chrX-116674063;