rs1339485

Positions:

• chrX-146281805-G-C
• chrX-146281805-G-T

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 0.422 in 110,353 control chromosomes in the GnomAD database, including 7,544 homozygotes. There are 13,369 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 0.42 (7544 hom., 13369 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.147

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.535 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.422 AC: 46496 AN: 110306 Hom.: 7538 Cov.: 23 AF XY: 0.409 AC XY: 13326 AN XY: 32618

Gnomad AFR AF: 0.542

Gnomad AMI AF: 0.450

Gnomad AMR AF: 0.527

Gnomad ASJ AF: 0.335

Gnomad EAS AF: 0.339

Gnomad SAS AF: 0.323

Gnomad FIN AF: 0.341

Gnomad MID AF: 0.353

Gnomad NFE AF: 0.355

Gnomad OTH AF: 0.420

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

GnomAD4 genome AF: 0.422 AC: 46558 AN: 110353 Hom.: 7544 Cov.: 23 AF XY: 0.409 AC XY: 13369 AN XY: 32675

Gnomad4 AFR AF: 0.542

Gnomad4 AMR AF: 0.528

Gnomad4 ASJ AF: 0.335

Gnomad4 EAS AF: 0.338

Gnomad4 SAS AF: 0.325

Gnomad4 FIN AF: 0.341

Gnomad4 NFE AF: 0.355

Gnomad4 OTH AF: 0.423

Alfa AF: 0.400 Hom.: 2614

Bravo AF: 0.451

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.15
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1339485; hg19: chrX-145363323;