rs1997625

chrX-71225931-T-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 0.52 (11192 hom., 16630 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.175

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BS2: High Homozygotes in GnomAd at 11184 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: 0.521 AC: 57351 AN: 109987 Hom.: 11184 Cov.: 22 AF XY: 0.514 AC XY: 16602 AN XY: 32299

Gnomad AFR AF: 0.389

Gnomad AMI AF: 0.680

Gnomad AMR AF: 0.407

Gnomad ASJ AF: 0.562

Gnomad EAS AF: 0.708

Gnomad SAS AF: 0.477

Gnomad FIN AF: 0.615

Gnomad MID AF: 0.593

Gnomad NFE AF: 0.595

Gnomad OTH AF: 0.513

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: 0.521 AC: 57379 AN: 110041 Hom.: 11192 Cov.: 22 AF XY: 0.514 AC XY: 16630 AN XY: 32363

Gnomad4 AFR AF: 0.389

Gnomad4 AMR AF: 0.406

Gnomad4 ASJ AF: 0.562

Gnomad4 EAS AF: 0.708

Gnomad4 SAS AF: 0.476

Gnomad4 FIN AF: 0.615

Gnomad4 NFE AF: 0.595

Gnomad4 OTH AF: 0.521

Alfa AF: 0.567 Hom.: 37352

Bravo AF: 0.502

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	5.5
Dann	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1997625; hg19: chrX-70445781;