chrX-100075518-A-G

Position:

• chrX-100075518-A-G

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 0.51 in 110,274 control chromosomes in the GnomAD database, including 12,615 homozygotes. There are 16,758 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 0.51 (12615 hom., 16758 hem., cov: 22)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.94

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.56).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.683 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.100075518A>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.510 AC: 56207 AN: 110222 Hom.: 12620 Cov.: 22 AF XY: 0.514 AC XY: 16745 AN XY: 32598

Gnomad AFR AF: 0.109

Gnomad AMI AF: 0.853

Gnomad AMR AF: 0.574

Gnomad ASJ AF: 0.570

Gnomad EAS AF: 0.523

Gnomad SAS AF: 0.611

Gnomad FIN AF: 0.773

Gnomad MID AF: 0.458

Gnomad NFE AF: 0.689

Gnomad OTH AF: 0.514

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

GnomAD4 genome AF: 0.510 AC: 56208 AN: 110274 Hom.: 12615 Cov.: 22 AF XY: 0.513 AC XY: 16758 AN XY: 32660

Gnomad4 AFR AF: 0.109

Gnomad4 AMR AF: 0.574

Gnomad4 ASJ AF: 0.570

Gnomad4 EAS AF: 0.524

Gnomad4 SAS AF: 0.611

Gnomad4 FIN AF: 0.773

Gnomad4 NFE AF: 0.689

Gnomad4 OTH AF: 0.519

Alfa AF: 0.577 Hom.: 6332

Bravo AF: 0.484

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.56
CADD	Benign	15
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs985251; hg19: chrX-99330516;