rs1339597

Variant names:

• chrX-145988145-G-A
• rs1339597

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.320 AC: 35586 AN: 111289 Hom.: 4087 Cov.: 23

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

African (AFR) AF: 0.302 AC: 9286 AN: 30718

American (AMR) AF: 0.347 AC: 3643 AN: 10502

Ashkenazi Jewish (ASJ) AF: 0.286 AC: 755 AN: 2643

East Asian (EAS) AF: 0.297 AC: 1042 AN: 3511

South Asian (SAS) AF: 0.389 AC: 1033 AN: 2658

European-Finnish (FIN) AF: 0.315 AC: 1873 AN: 5939

Middle Eastern (MID) AF: 0.324 AC: 70 AN: 216

European-Non Finnish (NFE) AF: 0.327 AC: 17318 AN: 52953

Other (OTH) AF: 0.325 AC: 492 AN: 1512

Alfa AF: 0.325 Hom.: 29788

Bravo AF: 0.323

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.0
DANN	Benign	0.42
PhyloP100		0.59

Splicing

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

Other links and lift over

dbSNP: rs1339597; hg19: chrX-145069663;