rs4827678

Variant names:

• chrX-145995800-G-A
• rs4827678

Your query was ambiguous. Multiple possible variants found:

• chrX-145995800-G-A
• chrX-145995800-G-C

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 0.61 (14897 hom., 19231 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.02
• Publications: 4 publications found

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.608 AC: 66730 AN: 109735 Hom.: 14889 Cov.: 22

Gnomad AFR AF: 0.745

Gnomad AMI AF: 0.419

Gnomad AMR AF: 0.552

Gnomad ASJ AF: 0.443

Gnomad EAS AF: 0.587

Gnomad SAS AF: 0.638

Gnomad FIN AF: 0.555

Gnomad MID AF: 0.574

Gnomad NFE AF: 0.558

Gnomad OTH AF: 0.583

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: 0.608 AC: 66773 AN: 109779 Hom.: 14897 Cov.: 22 AF XY: 0.599 AC XY: 19231 AN XY: 32103

African (AFR) AF: 0.745 AC: 22428 AN: 30113

American (AMR) AF: 0.553 AC: 5669 AN: 10259

Ashkenazi Jewish (ASJ) AF: 0.443 AC: 1164 AN: 2625

East Asian (EAS) AF: 0.587 AC: 2017 AN: 3439

South Asian (SAS) AF: 0.637 AC: 1614 AN: 2532

European-Finnish (FIN) AF: 0.555 AC: 3185 AN: 5735

Middle Eastern (MID) AF: 0.574 AC: 120 AN: 209

European-Non Finnish (NFE) AF: 0.558 AC: 29422 AN: 52702

Other (OTH) AF: 0.584 AC: 874 AN: 1496

Alfa AF: 0.577 Hom.: 71809

Bravo AF: 0.615

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.20
DANN	Benign	0.48
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs4827678; hg19: chrX-145077318;