rs1468111

Positions:

• chrX-745534-G-A
• chrX-745534-G-C
• chrX-745534-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0316 in 152,206 control chromosomes in the GnomAD database, including 95 homozygotes. There are 2,251 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 0.032 (95 hom., 2251 hem., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0316 (4810/152206) while in subpopulation AFR AF= 0.0451 (1874/41524). AF 95% confidence interval is 0.0434. There are 95 homozygotes in gnomad4. There are 2251 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 95 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.745534G>A		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0316 AC: 4806 AN: 152088 Hom.: 94 Cov.: 32 AF XY: 0.0302 AC XY: 2244 AN XY: 74278

Gnomad AFR AF: 0.0451

Gnomad AMI AF: 0.00220

Gnomad AMR AF: 0.0272

Gnomad ASJ AF: 0.0282

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00705

Gnomad FIN AF: 0.0218

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0306

Gnomad OTH AF: 0.0321

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

GnomAD4 genome AF: 0.0316 AC: 4810 AN: 152206 Hom.: 95 Cov.: 32 AF XY: 0.0303 AC XY: 2251 AN XY: 74406

Gnomad4 AFR AF: 0.0451

Gnomad4 AMR AF: 0.0271

Gnomad4 ASJ AF: 0.0282

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00747

Gnomad4 FIN AF: 0.0218

Gnomad4 NFE AF: 0.0306

Gnomad4 OTH AF: 0.0318

Bravo AF: 0.0326

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.0
DANN	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1468111; hg19: chrX-706269;