rs6525481

Variant names:

• chrX-71209374-C-G
• rs6525481

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 0.59 (14933 hom., 19391 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.431
• 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: 0.594 AC: 65652 AN: 110482 Hom.: 14924 Cov.: 23

Gnomad AFR AF: 0.821

Gnomad AMI AF: 0.661

Gnomad AMR AF: 0.625

Gnomad ASJ AF: 0.681

Gnomad EAS AF: 0.749

Gnomad SAS AF: 0.588

Gnomad FIN AF: 0.403

Gnomad MID AF: 0.660

Gnomad NFE AF: 0.463

Gnomad OTH AF: 0.618

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: 0.595 AC: 65715 AN: 110536 Hom.: 14933 Cov.: 23 AF XY: 0.591 AC XY: 19391 AN XY: 32808

African (AFR) AF: 0.821 AC: 24979 AN: 30412

American (AMR) AF: 0.625 AC: 6431 AN: 10290

Ashkenazi Jewish (ASJ) AF: 0.681 AC: 1790 AN: 2629

East Asian (EAS) AF: 0.748 AC: 2609 AN: 3486

South Asian (SAS) AF: 0.587 AC: 1549 AN: 2640

European-Finnish (FIN) AF: 0.403 AC: 2369 AN: 5883

Middle Eastern (MID) AF: 0.671 AC: 145 AN: 216

European-Non Finnish (NFE) AF: 0.463 AC: 24463 AN: 52809

Other (OTH) AF: 0.624 AC: 936 AN: 1499

Alfa AF: 0.541 Hom.: 4070

Bravo AF: 0.622

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.84
DANN	Benign	0.52
PhyloP100		-0.43

Splicing

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

Other links and lift over

dbSNP: rs6525481; hg19: chrX-70429224;