rs2214607

Positions:

• chrX-76185904-G-A
• chrX-76185904-G-T

Variant summary

Our verdict is Likely benign. Variant got -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 0.75 (22603 hom., 24276 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0750

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.751 AC: 82839 AN: 110262 Hom.: 22610 Cov.: 23 AF XY: 0.745 AC XY: 24212 AN XY: 32486

Gnomad AFR AF: 0.704

Gnomad AMI AF: 0.878

Gnomad AMR AF: 0.698

Gnomad ASJ AF: 0.840

Gnomad EAS AF: 0.221

Gnomad SAS AF: 0.664

Gnomad FIN AF: 0.814

Gnomad MID AF: 0.863

Gnomad NFE AF: 0.815

Gnomad OTH AF: 0.757

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: 0.751 AC: 82889 AN: 110316 Hom.: 22603 Cov.: 23 AF XY: 0.746 AC XY: 24276 AN XY: 32550

Gnomad4 AFR AF: 0.704

Gnomad4 AMR AF: 0.699

Gnomad4 ASJ AF: 0.840

Gnomad4 EAS AF: 0.221

Gnomad4 SAS AF: 0.667

Gnomad4 FIN AF: 0.814

Gnomad4 NFE AF: 0.815

Gnomad4 OTH AF: 0.750

Alfa AF: 0.792 Hom.: 82378

Bravo AF: 0.735

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2214607; hg19: chrX-75405739;