XR_001755842.2:n.3093C>T

Variant names:

• chrX-48638775-C-T
• rs1395950
• XR_001755842.2:n.3093C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_001755842.2(LOC107985695):​n.3093C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.411 in 110,319 control chromosomes in the GnomAD database, including 7,299 homozygotes. There are 12,894 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 0.41 (7299 hom., 12894 hem., cov: 22)
• Consequence: LOC107985695 XR_001755842.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.668
• Publications: 0 publications found

Genes affected

LOC107985695 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.566 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107985695	XR_001755842.2	n.3093C>T		non_coding_transcript_exon_variant	Exon 3 of 3
LOC107985695	XR_007068227.1	n.3089C>T		non_coding_transcript_exon_variant	Exon 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000232828	ENST00000746890.1	n.822-1708G>A		intron_variant	Intron 3 of 3
ENSG00000297322	ENST00000747099.1	n.349+1835C>T		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.411 AC: 45291 AN: 110263 Hom.: 7292 Cov.: 22

Gnomad AFR AF: 0.573

Gnomad AMI AF: 0.278

Gnomad AMR AF: 0.375

Gnomad ASJ AF: 0.213

Gnomad EAS AF: 0.437

Gnomad SAS AF: 0.338

Gnomad FIN AF: 0.337

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.348

Gnomad OTH AF: 0.368

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

GnomAD4 genome AF: 0.411 AC: 45344 AN: 110319 Hom.: 7299 Cov.: 22 AF XY: 0.396 AC XY: 12894 AN XY: 32599

African (AFR) AF: 0.574 AC: 17418 AN: 30366

American (AMR) AF: 0.376 AC: 3862 AN: 10276

Ashkenazi Jewish (ASJ) AF: 0.213 AC: 560 AN: 2626

East Asian (EAS) AF: 0.437 AC: 1530 AN: 3499

South Asian (SAS) AF: 0.337 AC: 895 AN: 2657

European-Finnish (FIN) AF: 0.337 AC: 1940 AN: 5760

Middle Eastern (MID) AF: 0.206 AC: 44 AN: 214

European-Non Finnish (NFE) AF: 0.348 AC: 18363 AN: 52760

Other (OTH) AF: 0.366 AC: 547 AN: 1495

Alfa AF: 0.270 Hom.: 1743

Bravo AF: 0.422

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.5
DANN	Benign	0.80
PhyloP100		-0.67

Splicing

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

Other links and lift over

dbSNP: rs1395950; hg19: chrX-48497163;