X-69134987-C-T

Variant names:

• chrX-69134987-C-T
• rs6625401
• ENST00000824576.1:n.793+5227C>T

Variant summary

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

The ENST00000824576.1(ENSG00000307210):​n.793+5227C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.36 in 109,968 control chromosomes in the GnomAD database, including 6,115 homozygotes. There are 11,668 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 0.36 (6115 hom., 11668 hem., cov: 22)
• Consequence: ENSG00000307210 ENST00000824576.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0310
• Publications: 2 publications found

Genes affected

ENSG00000307210 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.703 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000824576.1. 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
	ENSG00000307210	ENST00000824576.1		n.793+5227C>T		intron	N/A
	ENSG00000307210	ENST00000824577.1		n.788-988C>T		intron	N/A
	ENSG00000307210	ENST00000824578.1		n.388-988C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.361 AC: 39642 AN: 109910 Hom.: 6122 Cov.: 22

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.185

Gnomad AMR AF: 0.370

Gnomad ASJ AF: 0.550

Gnomad EAS AF: 0.727

Gnomad SAS AF: 0.685

Gnomad FIN AF: 0.409

Gnomad MID AF: 0.463

Gnomad NFE AF: 0.443

Gnomad OTH AF: 0.405

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

GnomAD4 genome AF: 0.360 AC: 39640 AN: 109968 Hom.: 6115 Cov.: 22 AF XY: 0.362 AC XY: 11668 AN XY: 32244

African (AFR) AF: 0.122 AC: 3697 AN: 30413

American (AMR) AF: 0.370 AC: 3801 AN: 10274

Ashkenazi Jewish (ASJ) AF: 0.550 AC: 1442 AN: 2621

East Asian (EAS) AF: 0.727 AC: 2483 AN: 3417

South Asian (SAS) AF: 0.688 AC: 1701 AN: 2471

European-Finnish (FIN) AF: 0.409 AC: 2340 AN: 5717

Middle Eastern (MID) AF: 0.442 AC: 92 AN: 208

European-Non Finnish (NFE) AF: 0.443 AC: 23346 AN: 52676

Other (OTH) AF: 0.410 AC: 613 AN: 1494

Alfa AF: 0.425 Hom.: 43417

Bravo AF: 0.352

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	15
DANN	Benign	0.80
PhyloP100		-0.031

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6625401;

hg19: chrX-68354830;