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. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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

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

African (AFR) AF: 0.0370 AC: 1136 AN: 30742

American (AMR) AF: 0.0468 AC: 491 AN: 10485

Ashkenazi Jewish (ASJ) AF: 0.0321 AC: 85 AN: 2645

East Asian (EAS) AF: 0.000850 AC: 3 AN: 3531

South Asian (SAS) AF: 0.0172 AC: 46 AN: 2668

European-Finnish (FIN) AF: 0.113 AC: 678 AN: 5990

Middle Eastern (MID) AF: 0.0465 AC: 10 AN: 215

European-Non Finnish (NFE) AF: 0.102 AC: 5430 AN: 53078

Other (OTH) AF: 0.0535 AC: 81 AN: 1514

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
PhyloP100		1.6

Splicing

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

Other links and lift over

dbSNP: rs719489; hg19: chrX-146870634;