chrX-80014183-G-A

Variant names:

• chrX-80014183-G-A
• rs7055763
• ENST00000772035.1:n.100-321C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000772035.1(ENSG00000300464):​n.100-321C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.109 in 109,552 control chromosomes in the GnomAD database, including 835 homozygotes. There are 3,546 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 0.11 (835 hom., 3546 hem., cov: 22)
• Consequence: ENSG00000300464 ENST00000772035.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.901
• Publications: 2 publications found

Genes affected

ENSG00000300464 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.466 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000772035.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000300464	ENST00000772035.1		n.100-321C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.108 AC: 11863 AN: 109506 Hom.: 834 Cov.: 22

Gnomad AFR AF: 0.210

Gnomad AMI AF: 0.0586

Gnomad AMR AF: 0.0868

Gnomad ASJ AF: 0.0213

Gnomad EAS AF: 0.486

Gnomad SAS AF: 0.130

Gnomad FIN AF: 0.102

Gnomad MID AF: 0.0466

Gnomad NFE AF: 0.0349

Gnomad OTH AF: 0.112

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

GnomAD4 genome AF: 0.109 AC: 11891 AN: 109552 Hom.: 835 Cov.: 22 AF XY: 0.111 AC XY: 3546 AN XY: 31964

African (AFR) AF: 0.211 AC: 6328 AN: 30056

American (AMR) AF: 0.0870 AC: 896 AN: 10302

Ashkenazi Jewish (ASJ) AF: 0.0213 AC: 56 AN: 2627

East Asian (EAS) AF: 0.486 AC: 1643 AN: 3383

South Asian (SAS) AF: 0.131 AC: 335 AN: 2559

European-Finnish (FIN) AF: 0.102 AC: 575 AN: 5655

Middle Eastern (MID) AF: 0.0558 AC: 12 AN: 215

European-Non Finnish (NFE) AF: 0.0349 AC: 1835 AN: 52607

Other (OTH) AF: 0.116 AC: 172 AN: 1482

Alfa AF: 0.0744 Hom.: 353

Bravo AF: 0.118

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.0
DANN	Benign	0.43
PhyloP100		-0.90

Splicing

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

Other links and lift over

dbSNP: rs7055763; hg19: chrX-79269682;