rs1155699

Positions:

• chrX-43391471-G-A

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

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 0.60 (14153 hom., 19192 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.253

Genes affected

(HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.43391471G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000285899	ENST00000649774.1	n.227-3814G>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.596 AC: 65719 AN: 110176 Hom.: 14155 Cov.: 22 AF XY: 0.590 AC XY: 19149 AN XY: 32472

Gnomad AFR AF: 0.498

Gnomad AMI AF: 0.539

Gnomad AMR AF: 0.702

Gnomad ASJ AF: 0.556

Gnomad EAS AF: 0.594

Gnomad SAS AF: 0.453

Gnomad FIN AF: 0.615

Gnomad MID AF: 0.647

Gnomad NFE AF: 0.640

Gnomad OTH AF: 0.600

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

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.597 AC: 65755 AN: 110228 Hom.: 14153 Cov.: 22 AF XY: 0.590 AC XY: 19192 AN XY: 32534

Gnomad4 AFR AF: 0.498

Gnomad4 AMR AF: 0.702

Gnomad4 ASJ AF: 0.556

Gnomad4 EAS AF: 0.595

Gnomad4 SAS AF: 0.455

Gnomad4 FIN AF: 0.615

Gnomad4 NFE AF: 0.640

Gnomad4 OTH AF: 0.600

Alfa AF: 0.625 Hom.: 7540

Bravo AF: 0.601

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.89
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1155699; hg19: chrX-43250720;