X-68986361-T-C

Variant names:

• chrX-68986361-T-C
• rs1277970
• ENST00000820668.1:n.206-5730A>G

Variant summary

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

The ENST00000820668.1(ENSG00000306747):​n.206-5730A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0307 in 111,901 control chromosomes in the GnomAD database, including 146 homozygotes. There are 930 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 0.031 (146 hom., 930 hem., cov: 23)
• Consequence: ENSG00000306747 ENST00000820668.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.02
• Publications: 1 publications found

Genes affected

ENSG00000306747 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.102 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000820668.1. 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
	ENSG00000306747	ENST00000820668.1		n.206-5730A>G		intron	N/A
	ENSG00000306747	ENST00000820669.1		n.701+1180A>G		intron	N/A
	ENSG00000306747	ENST00000820670.1		n.286+1180A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0307 AC: 3431 AN: 111851 Hom.: 147 Cov.: 23

Gnomad AFR AF: 0.105

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0127

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00112

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0211

Gnomad NFE AF: 0.000865

Gnomad OTH AF: 0.0232

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

GnomAD4 genome AF: 0.0307 AC: 3430 AN: 111901 Hom.: 146 Cov.: 23 AF XY: 0.0273 AC XY: 930 AN XY: 34077

African (AFR) AF: 0.105 AC: 3207 AN: 30670

American (AMR) AF: 0.0127 AC: 135 AN: 10625

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2646

East Asian (EAS) AF: 0.00 AC: 0 AN: 3539

South Asian (SAS) AF: 0.000751 AC: 2 AN: 2662

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 6137

Middle Eastern (MID) AF: 0.0231 AC: 5 AN: 216

European-Non Finnish (NFE) AF: 0.000865 AC: 46 AN: 53189

Other (OTH) AF: 0.0229 AC: 35 AN: 1529

Alfa AF: 0.0157 Hom.: 94

Bravo AF: 0.0366

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	9.1
DANN	Benign	0.77
PhyloP100		1.0

Splicing

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

Other links and lift over

dbSNP: rs1277970; hg19: chrX-68206204;