rs719489

Variant names:

• chrX-147789116-G-A
• rs719489

Your query was ambiguous. Multiple possible variants found:

• chrX-147789116-G-A
• chrX-147789116-G-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.0719 in 111,548 control chromosomes in the GnomAD database, including 275 homozygotes. There are 2,332 hemizygotes in GnomAD. 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 0.072 (275 hom., 2332 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.56

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.32).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.1 is higher than 0.05.

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: 0.0720 AC: 8026 AN: 111496 Hom.: 274 Cov.: 22 AF XY: 0.0693 AC XY: 2337 AN XY: 33718

Gnomad AFR AF: 0.0370

Gnomad AMI AF: 0.0926

Gnomad AMR AF: 0.0470

Gnomad ASJ AF: 0.0321

Gnomad EAS AF: 0.000847

Gnomad SAS AF: 0.0172

Gnomad FIN AF: 0.113

Gnomad MID AF: 0.0551

Gnomad NFE AF: 0.102

Gnomad OTH AF: 0.0542

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0719 AC: 8023 AN: 111548 Hom.: 275 Cov.: 22 AF XY: 0.0690 AC XY: 2332 AN XY: 33780

Gnomad4 AFR AF: 0.0370

Gnomad4 AMR AF: 0.0468

Gnomad4 ASJ AF: 0.0321

Gnomad4 EAS AF: 0.000850

Gnomad4 SAS AF: 0.0172

Gnomad4 FIN AF: 0.113

Gnomad4 NFE AF: 0.102

Gnomad4 OTH AF: 0.0535

Alfa AF: 0.0492 Hom.: 284

Bravo AF: 0.0670

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.32
CADD	Benign	9.7
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs719489; hg19: chrX-146870634;