rs1339597

Variant names:

• chrX-145988145-G-A
• rs1339597

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.32 in 111,339 control chromosomes in the GnomAD database, including 4,100 homozygotes. There are 10,450 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 0.32 (4100 hom., 10450 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.595

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.369 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: 0.320 AC: 35586 AN: 111289 Hom.: 4087 Cov.: 23 AF XY: 0.311 AC XY: 10436 AN XY: 33521

Gnomad AFR AF: 0.303

Gnomad AMI AF: 0.146

Gnomad AMR AF: 0.346

Gnomad ASJ AF: 0.286

Gnomad EAS AF: 0.297

Gnomad SAS AF: 0.388

Gnomad FIN AF: 0.315

Gnomad MID AF: 0.325

Gnomad NFE AF: 0.327

Gnomad OTH AF: 0.322

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

GnomAD4 genome AF: 0.320 AC: 35612 AN: 111339 Hom.: 4100 Cov.: 23 AF XY: 0.311 AC XY: 10450 AN XY: 33581

Gnomad4 AFR AF: 0.302

Gnomad4 AMR AF: 0.347

Gnomad4 ASJ AF: 0.286

Gnomad4 EAS AF: 0.297

Gnomad4 SAS AF: 0.389

Gnomad4 FIN AF: 0.315

Gnomad4 NFE AF: 0.327

Gnomad4 OTH AF: 0.325

Alfa AF: 0.324 Hom.: 22738

Bravo AF: 0.323

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.0
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1339597; hg19: chrX-145069663;