chrX-100609853-A-T

Variant names:

• chrX-100609853-A-T
• rs1204384
• XR_938469.2:n.37-3585T>A

Variant summary

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

The XR_938469.2(LOC105373298):​n.37-3585T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.35 in 110,901 control chromosomes in the GnomAD database, including 5,068 homozygotes. There are 11,379 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 0.35 (5068 hom., 11379 hem., cov: 23)
• Consequence: LOC105373298 XR_938469.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.37
• Publications: 1 publications found

Genes affected

LOC105373298 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.676 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.350 AC: 38754 AN: 110849 Hom.: 5064 Cov.: 23

Gnomad AFR AF: 0.302

Gnomad AMI AF: 0.456

Gnomad AMR AF: 0.435

Gnomad ASJ AF: 0.382

Gnomad EAS AF: 0.699

Gnomad SAS AF: 0.344

Gnomad FIN AF: 0.290

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.339

Gnomad OTH AF: 0.406

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

GnomAD4 genome AF: 0.350 AC: 38784 AN: 110901 Hom.: 5068 Cov.: 23 AF XY: 0.343 AC XY: 11379 AN XY: 33159

African (AFR) AF: 0.302 AC: 9259 AN: 30625

American (AMR) AF: 0.435 AC: 4525 AN: 10393

Ashkenazi Jewish (ASJ) AF: 0.382 AC: 1005 AN: 2633

East Asian (EAS) AF: 0.699 AC: 2450 AN: 3505

South Asian (SAS) AF: 0.344 AC: 896 AN: 2604

European-Finnish (FIN) AF: 0.290 AC: 1719 AN: 5926

Middle Eastern (MID) AF: 0.404 AC: 86 AN: 213

European-Non Finnish (NFE) AF: 0.339 AC: 17923 AN: 52836

Other (OTH) AF: 0.411 AC: 616 AN: 1497

Alfa AF: 0.191 Hom.: 922

Bravo AF: 0.369

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	7.6
DANN	Benign	0.57
PhyloP100		2.4

Splicing

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

Other links and lift over

dbSNP: rs1204384; hg19: chrX-99864850;