X-100609853-A-T

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

LOC105373298 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105373298	XR_938469.2	n.37-3585T>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.350 AC: 38754 AN: 110849 Hom.: 5064 Cov.: 23 AF XY: 0.343 AC XY: 11357 AN XY: 33097

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

Gnomad4 AFR AF: 0.302

Gnomad4 AMR AF: 0.435

Gnomad4 ASJ AF: 0.382

Gnomad4 EAS AF: 0.699

Gnomad4 SAS AF: 0.344

Gnomad4 FIN AF: 0.290

Gnomad4 NFE AF: 0.339

Gnomad4 OTH AF: 0.411

Alfa AF: 0.191 Hom.: 922

Bravo AF: 0.369

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1204384; hg19: chrX-99864850;