rs6625163

chrX-67291142-G-AchrX-67291142-G-C

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_Strong BS2

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 0.64 (19206 hom., 20534 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.130

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BS2: High Homozygotes in GnomAd at 19215 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.637 AC: 69381 AN: 108944 Hom.: 19215 Cov.: 22 AF XY: 0.654 AC XY: 20530 AN XY: 31374

Gnomad AFR AF: 0.136

Gnomad AMI AF: 0.877

Gnomad AMR AF: 0.820

Gnomad ASJ AF: 0.896

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.914

Gnomad FIN AF: 0.813

Gnomad MID AF: 0.768

Gnomad NFE AF: 0.814

Gnomad OTH AF: 0.682

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: 0.636 AC: 69361 AN: 108980 Hom.: 19206 Cov.: 22 AF XY: 0.654 AC XY: 20534 AN XY: 31420

Gnomad4 AFR AF: 0.136

Gnomad4 AMR AF: 0.821

Gnomad4 ASJ AF: 0.896

Gnomad4 EAS AF: 0.998

Gnomad4 SAS AF: 0.914

Gnomad4 FIN AF: 0.813

Gnomad4 NFE AF: 0.814

Gnomad4 OTH AF: 0.685

Alfa AF: 0.809 Hom.: 88532

Bravo AF: 0.620

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	1.3
Dann	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6625163; hg19: chrX-66510984;