X-78916693-C-T

Position:

• chrX-78916693-C-T

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 0.0592 in 111,361 control chromosomes in the GnomAD database, including 597 homozygotes. There are 2,253 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 0.059 (597 hom., 2253 hem., cov: 23)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.820

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 (EAS) allele frequency at 95% confidence interval = 0.469 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.78916693C>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0592 AC: 6589 AN: 111306 Hom.: 595 Cov.: 23 AF XY: 0.0670 AC XY: 2249 AN XY: 33544

Gnomad AFR AF: 0.0114

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.228

Gnomad ASJ AF: 0.0390

Gnomad EAS AF: 0.488

Gnomad SAS AF: 0.266

Gnomad FIN AF: 0.0181

Gnomad MID AF: 0.00847

Gnomad NFE AF: 0.0210

Gnomad OTH AF: 0.0726

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

GnomAD4 genome AF: 0.0592 AC: 6596 AN: 111361 Hom.: 597 Cov.: 23 AF XY: 0.0670 AC XY: 2253 AN XY: 33609

Gnomad4 AFR AF: 0.0114

Gnomad4 AMR AF: 0.229

Gnomad4 ASJ AF: 0.0390

Gnomad4 EAS AF: 0.488

Gnomad4 SAS AF: 0.266

Gnomad4 FIN AF: 0.0181

Gnomad4 NFE AF: 0.0210

Gnomad4 OTH AF: 0.0736

Alfa AF: 0.0430 Hom.: 244

Bravo AF: 0.0786

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.64
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10521387; hg19: chrX-78172190;