chrX-67140772-T-C

Variant names:

• chrX-67140772-T-C
• rs5919287

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 (20423 hom., 21605 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.397
• Publications: 2 publications found

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).

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: 0.657 AC: 72283 AN: 109971 Hom.: 20430 Cov.: 22

Gnomad AFR AF: 0.155

Gnomad AMI AF: 0.887

Gnomad AMR AF: 0.829

Gnomad ASJ AF: 0.920

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.917

Gnomad FIN AF: 0.828

Gnomad MID AF: 0.763

Gnomad NFE AF: 0.843

Gnomad OTH AF: 0.702

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: 0.657 AC: 72278 AN: 110025 Hom.: 20423 Cov.: 22 AF XY: 0.667 AC XY: 21605 AN XY: 32415

African (AFR) AF: 0.155 AC: 4733 AN: 30487

American (AMR) AF: 0.829 AC: 8460 AN: 10201

Ashkenazi Jewish (ASJ) AF: 0.920 AC: 2413 AN: 2622

East Asian (EAS) AF: 0.999 AC: 3424 AN: 3429

South Asian (SAS) AF: 0.917 AC: 2325 AN: 2536

European-Finnish (FIN) AF: 0.828 AC: 4786 AN: 5777

Middle Eastern (MID) AF: 0.759 AC: 164 AN: 216

European-Non Finnish (NFE) AF: 0.843 AC: 44322 AN: 52587

Other (OTH) AF: 0.704 AC: 1049 AN: 1491

Alfa AF: 0.758 Hom.: 29907

Bravo AF: 0.641

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.2
DANN	Benign	0.42
PhyloP100		-0.40

Splicing

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

Other links and lift over

dbSNP: rs5919287; hg19: chrX-66360614;