X-71186069-T-C

Variant names:

• chrX-71186069-T-C
• rs6624538
• ENST00000450860.1:n.268-2052A>G

Variant summary

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

The ENST00000450860.1(ENSG00000228427):​n.268-2052A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.51 (10689 hom., 11597 hem., cov: 17)
• Consequence: ENSG00000228427 ENST00000450860.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.30
• Publications: 1 publications found

Genes affected

ENSG00000228427 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.684 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000450860.1. 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
	ENSG00000228427	ENST00000450860.1	TSL:3	n.268-2052A>G		intron	N/A
	ENSG00000228427	ENST00000652147.3		n.358-2056A>G		intron	N/A
	ENSG00000228427	ENST00000664514.4		n.600-2052A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.506 AC: 50404 AN: 99682 Hom.: 10685 Cov.: 17

Gnomad AFR AF: 0.692

Gnomad AMI AF: 0.502

Gnomad AMR AF: 0.576

Gnomad ASJ AF: 0.599

Gnomad EAS AF: 0.708

Gnomad SAS AF: 0.551

Gnomad FIN AF: 0.350

Gnomad MID AF: 0.612

Gnomad NFE AF: 0.383

Gnomad OTH AF: 0.555

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

GnomAD4 genome AF: 0.506 AC: 50433 AN: 99708 Hom.: 10689 Cov.: 17 AF XY: 0.490 AC XY: 11597 AN XY: 23660

African (AFR) AF: 0.693 AC: 18836 AN: 27195

American (AMR) AF: 0.576 AC: 5163 AN: 8968

Ashkenazi Jewish (ASJ) AF: 0.599 AC: 1494 AN: 2496

East Asian (EAS) AF: 0.707 AC: 2172 AN: 3070

South Asian (SAS) AF: 0.551 AC: 1121 AN: 2033

European-Finnish (FIN) AF: 0.350 AC: 1535 AN: 4380

Middle Eastern (MID) AF: 0.632 AC: 122 AN: 193

European-Non Finnish (NFE) AF: 0.383 AC: 18928 AN: 49421

Other (OTH) AF: 0.563 AC: 752 AN: 1335

Alfa AF: 0.159 Hom.: 485

Bravo AF: 0.537

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.42
DANN	Benign	0.17
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs6624538; hg19: chrX-70405919;