X-8426212-A-G

Position:

• chrX-8426212-A-G

Variant summary

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

The XR_001755783.2(LOC107985675):​n.6225+886A>G 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 0.59 (14363 hom., 18260 hem., cov: 21)
  • Failed GnomAD Quality Control
• Consequence: LOC107985675 XR_001755783.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.502

Genes affected

LOC107985675 (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	UniProt
LOC107985675	XR_001755783.2	n.6225+886A>G		intron_variant, non_coding_transcript_variant
LOC107985675	XR_001755782.2	n.1986-13616A>G		intron_variant, non_coding_transcript_variant
LOC107985675	XR_001755784.2	n.1986-13616A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.595 AC: 64807 AN: 108972 Hom.: 14364 Cov.: 21 AF XY: 0.582 AC XY: 18205 AN XY: 31306

Gnomad AFR AF: 0.744

Gnomad AMI AF: 0.637

Gnomad AMR AF: 0.649

Gnomad ASJ AF: 0.499

Gnomad EAS AF: 0.669

Gnomad SAS AF: 0.451

Gnomad FIN AF: 0.505

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.516

Gnomad OTH AF: 0.591

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: 0.595 AC: 64860 AN: 109031 Hom.: 14363 Cov.: 21 AF XY: 0.582 AC XY: 18260 AN XY: 31373

Gnomad4 AFR AF: 0.744

Gnomad4 AMR AF: 0.648

Gnomad4 ASJ AF: 0.499

Gnomad4 EAS AF: 0.669

Gnomad4 SAS AF: 0.452

Gnomad4 FIN AF: 0.505

Gnomad4 NFE AF: 0.516

Gnomad4 OTH AF: 0.593

Alfa AF: 0.534 Hom.: 58929

Bravo AF: 0.615

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.4
DANN	Benign	0.22

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7892812; hg19: chrX-8394253;