rs6647911

Variant names:

• chrX-76067659-A-G
• rs6647911

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 0.91 (33186 hom., 29273 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08
• 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=-0.96).

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: 0.909 AC: 100321 AN: 110386 Hom.: 33192 Cov.: 22

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

African (AFR) AF: 0.907 AC: 27545 AN: 30377

American (AMR) AF: 0.807 AC: 8333 AN: 10324

Ashkenazi Jewish (ASJ) AF: 0.974 AC: 2566 AN: 2634

East Asian (EAS) AF: 0.230 AC: 801 AN: 3488

South Asian (SAS) AF: 0.763 AC: 1961 AN: 2569

European-Finnish (FIN) AF: 0.953 AC: 5483 AN: 5756

Middle Eastern (MID) AF: 0.991 AC: 214 AN: 216

European-Non Finnish (NFE) AF: 0.972 AC: 51425 AN: 52895

Other (OTH) AF: 0.910 AC: 1362 AN: 1497

Alfa AF: 0.941 Hom.: 88320

Bravo AF: 0.888

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.1
DANN	Benign	0.42
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs6647911; hg19: chrX-75287494;