X-69134987-C-T

Position:

• chrX-69134987-C-T

Variant summary

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

The XR_001755985.2(LOC107985646):​n.295-988C>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 0.36 in 109,968 control chromosomes in the GnomAD database, including 6,115 homozygotes. There are 11,668 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 0.36 (6115 hom., 11668 hem., cov: 22)
• Consequence: LOC107985646 XR_001755985.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0310

Genes affected

LOC107985646 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.703 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107985646	XR_001755985.2	n.295-988C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.361 AC: 39642 AN: 109910 Hom.: 6122 Cov.: 22 AF XY: 0.362 AC XY: 11653 AN XY: 32176

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.185

Gnomad AMR AF: 0.370

Gnomad ASJ AF: 0.550

Gnomad EAS AF: 0.727

Gnomad SAS AF: 0.685

Gnomad FIN AF: 0.409

Gnomad MID AF: 0.463

Gnomad NFE AF: 0.443

Gnomad OTH AF: 0.405

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

GnomAD4 genome AF: 0.360 AC: 39640 AN: 109968 Hom.: 6115 Cov.: 22 AF XY: 0.362 AC XY: 11668 AN XY: 32244

Gnomad4 AFR AF: 0.122

Gnomad4 AMR AF: 0.370

Gnomad4 ASJ AF: 0.550

Gnomad4 EAS AF: 0.727

Gnomad4 SAS AF: 0.688

Gnomad4 FIN AF: 0.409

Gnomad4 NFE AF: 0.443

Gnomad4 OTH AF: 0.410

Alfa AF: 0.441 Hom.: 34767

Bravo AF: 0.352

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	15
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6625401; hg19: chrX-68354830;