chrX-145361034-A-C

Position:

• chrX-145361034-A-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.071 in 111,134 control chromosomes in the GnomAD database, including 242 homozygotes. There are 2,462 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 0.071 (242 hom., 2462 hem., cov: 23)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.835

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0914 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.145361034A>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0710 AC: 7890 AN: 111090 Hom.: 241 Cov.: 23 AF XY: 0.0739 AC XY: 2461 AN XY: 33304

Gnomad AFR AF: 0.0174

Gnomad AMI AF: 0.0513

Gnomad AMR AF: 0.0786

Gnomad ASJ AF: 0.0928

Gnomad EAS AF: 0.0279

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.149

Gnomad MID AF: 0.148

Gnomad NFE AF: 0.0917

Gnomad OTH AF: 0.0866

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

GnomAD4 genome AF: 0.0710 AC: 7888 AN: 111134 Hom.: 242 Cov.: 23 AF XY: 0.0738 AC XY: 2462 AN XY: 33358

Gnomad4 AFR AF: 0.0174

Gnomad4 AMR AF: 0.0785

Gnomad4 ASJ AF: 0.0928

Gnomad4 EAS AF: 0.0277

Gnomad4 SAS AF: 0.101

Gnomad4 FIN AF: 0.149

Gnomad4 NFE AF: 0.0917

Gnomad4 OTH AF: 0.0855

Alfa AF: 0.0886 Hom.: 3399

Bravo AF: 0.0642

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.7
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs580628; hg19: chrX-144442552;