chrX-115345861-C-T

Position:

• chrX-115345861-C-T

Variant summary

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

The XR_001755944.2(LOC107985681):​n.2354C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. 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 0.84 (27540 hom., 27573 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: LOC107985681 XR_001755944.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.607

Genes affected

LOC107985681 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107985681	XR_001755944.2	n.2354C>T		non_coding_transcript_exon_variant	1/3
		n.115345861C>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.843 AC: 92912 AN: 110171 Hom.: 27542 Cov.: 22 AF XY: 0.850 AC XY: 27521 AN XY: 32389

Gnomad AFR AF: 0.852

Gnomad AMI AF: 0.871

Gnomad AMR AF: 0.867

Gnomad ASJ AF: 0.791

Gnomad EAS AF: 0.948

Gnomad SAS AF: 0.947

Gnomad FIN AF: 0.874

Gnomad MID AF: 0.845

Gnomad NFE AF: 0.821

Gnomad OTH AF: 0.848

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: 0.843 AC: 92959 AN: 110224 Hom.: 27540 Cov.: 22 AF XY: 0.850 AC XY: 27573 AN XY: 32452

Gnomad4 AFR AF: 0.851

Gnomad4 AMR AF: 0.867

Gnomad4 ASJ AF: 0.791

Gnomad4 EAS AF: 0.948

Gnomad4 SAS AF: 0.948

Gnomad4 FIN AF: 0.874

Gnomad4 NFE AF: 0.821

Gnomad4 OTH AF: 0.850

Alfa AF: 0.833 Hom.: 8143

Bravo AF: 0.846

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	6.4

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1884396; hg19: chrX-114580445;