rs719489

Positions:

• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;