X-83492771-G-A

Position:

• chrX-83492771-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_001755986.2(LOC107985635):​n.145-863C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.417 in 110,608 control chromosomes in the GnomAD database, including 7,652 homozygotes. There are 13,603 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 (7652 hom., 13603 hem., cov: 23)
• Consequence: LOC107985635 XR_001755986.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.920

Genes affected

LOC107985635 (HGNC:):

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 (EAS) allele frequency at 95% confidence interval = 0.595 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107985635	XR_001755986.2	n.145-863C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.418 AC: 46172 AN: 110556 Hom.: 7661 Cov.: 23 AF XY: 0.414 AC XY: 13601 AN XY: 32860

Gnomad AFR AF: 0.217

Gnomad AMI AF: 0.494

Gnomad AMR AF: 0.364

Gnomad ASJ AF: 0.560

Gnomad EAS AF: 0.616

Gnomad SAS AF: 0.301

Gnomad FIN AF: 0.566

Gnomad MID AF: 0.507

Gnomad NFE AF: 0.512

Gnomad OTH AF: 0.444

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

GnomAD4 genome AF: 0.417 AC: 46148 AN: 110608 Hom.: 7652 Cov.: 23 AF XY: 0.413 AC XY: 13603 AN XY: 32924

Gnomad4 AFR AF: 0.217

Gnomad4 AMR AF: 0.363

Gnomad4 ASJ AF: 0.560

Gnomad4 EAS AF: 0.617

Gnomad4 SAS AF: 0.299

Gnomad4 FIN AF: 0.566

Gnomad4 NFE AF: 0.512

Gnomad4 OTH AF: 0.438

Alfa AF: 0.471 Hom.: 11637

Bravo AF: 0.400

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.12
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5968183; hg19: chrX-82747779;