XR_001755952.1:n.858+312G>A

Variant names:

• chrX-127248230-C-T
• rs201647
• XR_001755952.1:n.858+312G>A

Variant summary

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

The XR_001755952.1(LOC107985709):​n.858+312G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0303 in 111,594 control chromosomes in the GnomAD database, including 92 homozygotes. There are 973 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 0.030 (92 hom., 973 hem., cov: 23)
• Consequence: LOC107985709 XR_001755952.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.77
• Publications: 2 publications found

Genes affected

LOC107985709 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.086 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.0302 AC: 3367 AN: 111542 Hom.: 93 Cov.: 23

Gnomad AFR AF: 0.0885

Gnomad AMI AF: 0.00440

Gnomad AMR AF: 0.0234

Gnomad ASJ AF: 0.0212

Gnomad EAS AF: 0.00197

Gnomad SAS AF: 0.0442

Gnomad FIN AF: 0.000167

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.00311

Gnomad OTH AF: 0.0341

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

GnomAD4 genome AF: 0.0303 AC: 3378 AN: 111594 Hom.: 92 Cov.: 23 AF XY: 0.0288 AC XY: 973 AN XY: 33810

African (AFR) AF: 0.0888 AC: 2727 AN: 30708

American (AMR) AF: 0.0233 AC: 244 AN: 10476

Ashkenazi Jewish (ASJ) AF: 0.0212 AC: 56 AN: 2643

East Asian (EAS) AF: 0.00197 AC: 7 AN: 3549

South Asian (SAS) AF: 0.0440 AC: 119 AN: 2702

European-Finnish (FIN) AF: 0.000167 AC: 1 AN: 5986

Middle Eastern (MID) AF: 0.0276 AC: 6 AN: 217

European-Non Finnish (NFE) AF: 0.00309 AC: 164 AN: 53118

Other (OTH) AF: 0.0337 AC: 51 AN: 1513

Alfa AF: 0.0209 Hom.: 94

Bravo AF: 0.0369

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.047
DANN	Benign	0.19
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs201647; hg19: chrX-126382213;