X-71206075-C-T

Variant names:

• chrX-71206075-C-T
• rs35328964

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 (15000 hom., 17163 hem., cov: 20)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.47
• 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=-1.01).

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: 0.593 AC: 63447 AN: 106924 Hom.: 14991 Cov.: 20

Gnomad AFR AF: 0.823

Gnomad AMI AF: 0.667

Gnomad AMR AF: 0.625

Gnomad ASJ AF: 0.677

Gnomad EAS AF: 0.745

Gnomad SAS AF: 0.591

Gnomad FIN AF: 0.378

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.464

Gnomad OTH AF: 0.624

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: 0.594 AC: 63506 AN: 106974 Hom.: 15000 Cov.: 20 AF XY: 0.582 AC XY: 17163 AN XY: 29514

African (AFR) AF: 0.823 AC: 24079 AN: 29263

American (AMR) AF: 0.625 AC: 6122 AN: 9788

Ashkenazi Jewish (ASJ) AF: 0.677 AC: 1759 AN: 2597

East Asian (EAS) AF: 0.745 AC: 2515 AN: 3375

South Asian (SAS) AF: 0.590 AC: 1437 AN: 2437

European-Finnish (FIN) AF: 0.378 AC: 1968 AN: 5210

Middle Eastern (MID) AF: 0.675 AC: 141 AN: 209

European-Non Finnish (NFE) AF: 0.464 AC: 24122 AN: 51969

Other (OTH) AF: 0.629 AC: 919 AN: 1460

Alfa AF: 0.525 Hom.: 3741

Bravo AF: 0.625

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.15
DANN	Benign	0.54
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs35328964; hg19: chrX-70425925;