X-8107901-C-T

Variant names:

• chrX-8107901-C-T
• rs1869588
• ENST00000649338.1:n.262+9726C>T

Variant summary

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

The ENST00000649338.1(ENSG00000285679):​n.262+9726C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.413 in 110,774 control chromosomes in the GnomAD database, including 6,963 homozygotes. There are 13,392 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 (6963 hom., 13392 hem., cov: 23)
• Consequence: ENSG00000285679 ENST00000649338.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02
• Publications: 3 publications found

Genes affected

ENSG00000285679 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.723 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107985675	XR_001755782.2	n.1915-120434C>T		intron_variant	Intron 1 of 3
LOC107985675	XR_001755783.2	n.1915-120434C>T		intron_variant	Intron 1 of 4
LOC107985675	XR_001755784.2	n.1915-120434C>T		intron_variant	Intron 1 of 4
LOC107985675	XR_007068387.1	n.1915-120434C>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285679	ENST00000649338.1	n.262+9726C>T		intron_variant	Intron 3 of 4
ENSG00000285679	ENST00000659022.1	n.972-120434C>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.413 AC: 45697 AN: 110720 Hom.: 6959 Cov.: 23

Gnomad AFR AF: 0.375

Gnomad AMI AF: 0.351

Gnomad AMR AF: 0.454

Gnomad ASJ AF: 0.334

Gnomad EAS AF: 0.746

Gnomad SAS AF: 0.455

Gnomad FIN AF: 0.368

Gnomad MID AF: 0.403

Gnomad NFE AF: 0.411

Gnomad OTH AF: 0.432

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

GnomAD4 genome AF: 0.413 AC: 45717 AN: 110774 Hom.: 6963 Cov.: 23 AF XY: 0.405 AC XY: 13392 AN XY: 33044

African (AFR) AF: 0.375 AC: 11418 AN: 30459

American (AMR) AF: 0.455 AC: 4756 AN: 10445

Ashkenazi Jewish (ASJ) AF: 0.334 AC: 881 AN: 2635

East Asian (EAS) AF: 0.747 AC: 2575 AN: 3447

South Asian (SAS) AF: 0.456 AC: 1197 AN: 2625

European-Finnish (FIN) AF: 0.368 AC: 2171 AN: 5901

Middle Eastern (MID) AF: 0.400 AC: 86 AN: 215

European-Non Finnish (NFE) AF: 0.411 AC: 21742 AN: 52853

Other (OTH) AF: 0.430 AC: 656 AN: 1525

Alfa AF: 0.413 Hom.: 14081

Bravo AF: 0.421

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.40
DANN	Benign	0.33
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs1869588; hg19: chrX-8075942;