rs6647911

Positions:

• chrX-76067659-A-G

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 0.91 (33186 hom., 29273 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08

Genes affected

(HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.76067659A>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.909 AC: 100321 AN: 110386 Hom.: 33192 Cov.: 22 AF XY: 0.897 AC XY: 29211 AN XY: 32556

Gnomad AFR AF: 0.907

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.807

Gnomad ASJ AF: 0.974

Gnomad EAS AF: 0.230

Gnomad SAS AF: 0.762

Gnomad FIN AF: 0.953

Gnomad MID AF: 0.987

Gnomad NFE AF: 0.972

Gnomad OTH AF: 0.911

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: 0.909 AC: 100373 AN: 110439 Hom.: 33186 Cov.: 22 AF XY: 0.897 AC XY: 29273 AN XY: 32619

Gnomad4 AFR AF: 0.907

Gnomad4 AMR AF: 0.807

Gnomad4 ASJ AF: 0.974

Gnomad4 EAS AF: 0.230

Gnomad4 SAS AF: 0.763

Gnomad4 FIN AF: 0.953

Gnomad4 NFE AF: 0.972

Gnomad4 OTH AF: 0.910

Alfa AF: 0.945 Hom.: 61625

Bravo AF: 0.888

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.1
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6647911; hg19: chrX-75287494;