rs177008

Variant names:

• chrX-125567397-A-G
• rs177008

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 0.66 (17259 hom., 21444 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36
• Publications: 1 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: 0.664 AC: 73116 AN: 110069 Hom.: 17259 Cov.: 22

Gnomad AFR AF: 0.599

Gnomad AMI AF: 0.623

Gnomad AMR AF: 0.697

Gnomad ASJ AF: 0.687

Gnomad EAS AF: 0.897

Gnomad SAS AF: 0.723

Gnomad FIN AF: 0.669

Gnomad MID AF: 0.715

Gnomad NFE AF: 0.676

Gnomad OTH AF: 0.671

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: 0.664 AC: 73155 AN: 110119 Hom.: 17259 Cov.: 22 AF XY: 0.662 AC XY: 21444 AN XY: 32401

African (AFR) AF: 0.600 AC: 18183 AN: 30321

American (AMR) AF: 0.697 AC: 7239 AN: 10383

Ashkenazi Jewish (ASJ) AF: 0.687 AC: 1801 AN: 2622

East Asian (EAS) AF: 0.897 AC: 3073 AN: 3427

South Asian (SAS) AF: 0.724 AC: 1813 AN: 2505

European-Finnish (FIN) AF: 0.669 AC: 3870 AN: 5787

Middle Eastern (MID) AF: 0.720 AC: 154 AN: 214

European-Non Finnish (NFE) AF: 0.676 AC: 35609 AN: 52709

Other (OTH) AF: 0.672 AC: 999 AN: 1486

Alfa AF: 0.671 Hom.: 72602

Bravo AF: 0.666

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.74
DANN	Benign	0.43
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs177008; hg19: chrX-124701246;