X-94590840-C-T

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_Strong BS2

The XR_001755915.2(LOC107985704):n.219+9267G>A variant causes a intron, non coding transcript 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 0.64 (16972 hom., 20179 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: LOC107985704 XR_001755915.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.799

Genes affected

LOC107985704 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BS2: High Homozygotes in GnomAd at 16980 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107985704	XR_001755915.2	n.219+9267G>A		intron_variant, non_coding_transcript_variant
LOC107985704	XR_001755914.2	n.219+9267G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.636 AC: 70105 AN: 110254 Hom.: 16980 Cov.: 23 AF XY: 0.620 AC XY: 20158 AN XY: 32514

Gnomad AFR AF: 0.599

Gnomad AMI AF: 0.726

Gnomad AMR AF: 0.424

Gnomad ASJ AF: 0.811

Gnomad EAS AF: 0.0170

Gnomad SAS AF: 0.378

Gnomad FIN AF: 0.760

Gnomad MID AF: 0.668

Gnomad NFE AF: 0.730

Gnomad OTH AF: 0.626

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: 0.636 AC: 70109 AN: 110310 Hom.: 16972 Cov.: 23 AF XY: 0.619 AC XY: 20179 AN XY: 32580

Gnomad4 AFR AF: 0.598

Gnomad4 AMR AF: 0.424

Gnomad4 ASJ AF: 0.811

Gnomad4 EAS AF: 0.0171

Gnomad4 SAS AF: 0.380

Gnomad4 FIN AF: 0.760

Gnomad4 NFE AF: 0.730

Gnomad4 OTH AF: 0.618

Alfa AF: 0.682 Hom.: 17735

Bravo AF: 0.606

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	2.8
Dann	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5950049; hg19: chrX-93845839;