chrX-131266334-C-A

Variant names:

• chrX-131266334-C-A
• rs6637820
• ENST00000773800.1:n.560+46861C>A

Variant summary

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

The ENST00000773800.1(ENSG00000287806):​n.560+46861C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.136 in 109,951 control chromosomes in the GnomAD database, including 1,254 homozygotes. There are 4,524 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 0.14 (1254 hom., 4524 hem., cov: 22)
• Consequence: ENSG00000287806 ENST00000773800.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.359
• Publications: 3 publications found

Genes affected

ENSG00000287806 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.727 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000773800.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000287806	ENST00000773800.1		n.560+46861C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.136 AC: 14951 AN: 109897 Hom.: 1256 Cov.: 22

Gnomad AFR AF: 0.157

Gnomad AMI AF: 0.0616

Gnomad AMR AF: 0.190

Gnomad ASJ AF: 0.0739

Gnomad EAS AF: 0.751

Gnomad SAS AF: 0.260

Gnomad FIN AF: 0.107

Gnomad MID AF: 0.0979

Gnomad NFE AF: 0.0754

Gnomad OTH AF: 0.126

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

GnomAD4 genome AF: 0.136 AC: 14952 AN: 109951 Hom.: 1254 Cov.: 22 AF XY: 0.140 AC XY: 4524 AN XY: 32293

African (AFR) AF: 0.157 AC: 4731 AN: 30218

American (AMR) AF: 0.190 AC: 1934 AN: 10200

Ashkenazi Jewish (ASJ) AF: 0.0739 AC: 194 AN: 2626

East Asian (EAS) AF: 0.752 AC: 2593 AN: 3450

South Asian (SAS) AF: 0.259 AC: 651 AN: 2510

European-Finnish (FIN) AF: 0.107 AC: 615 AN: 5734

Middle Eastern (MID) AF: 0.0884 AC: 19 AN: 215

European-Non Finnish (NFE) AF: 0.0754 AC: 3983 AN: 52817

Other (OTH) AF: 0.127 AC: 190 AN: 1499

Alfa AF: 0.101 Hom.: 9383

Bravo AF: 0.153

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.011
DANN	Benign	0.42
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs6637820; hg19: chrX-130400308;