X-112864517-G-C

Variant names:

• chrX-112864517-G-C
• rs547425
• ENST00000738665.1:n.277+17438G>C

Variant summary

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

The ENST00000738665.1(ENSG00000286072):​n.277+17438G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.353 in 110,786 control chromosomes in the GnomAD database, including 5,946 homozygotes. There are 11,380 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 0.35 (5946 hom., 11380 hem., cov: 23)
• Consequence: ENSG00000286072 ENST00000738665.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.166
• Publications: 0 publications found

Genes affected

ENSG00000286072 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.563 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000738665.1. 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
	ENSG00000286072	ENST00000738665.1		n.277+17438G>C		intron	N/A
	ENSG00000286072	ENST00000738666.1		n.396+17438G>C		intron	N/A
	ENSG00000286072	ENST00000738667.1		n.410+17438G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.353 AC: 39043 AN: 110734 Hom.: 5942 Cov.: 23

Gnomad AFR AF: 0.542

Gnomad AMI AF: 0.202

Gnomad AMR AF: 0.472

Gnomad ASJ AF: 0.139

Gnomad EAS AF: 0.585

Gnomad SAS AF: 0.184

Gnomad FIN AF: 0.306

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.233

Gnomad OTH AF: 0.336

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

GnomAD4 genome AF: 0.353 AC: 39069 AN: 110786 Hom.: 5946 Cov.: 23 AF XY: 0.344 AC XY: 11380 AN XY: 33050

African (AFR) AF: 0.542 AC: 16447 AN: 30363

American (AMR) AF: 0.472 AC: 4914 AN: 10405

Ashkenazi Jewish (ASJ) AF: 0.139 AC: 366 AN: 2638

East Asian (EAS) AF: 0.584 AC: 2040 AN: 3492

South Asian (SAS) AF: 0.183 AC: 479 AN: 2620

European-Finnish (FIN) AF: 0.306 AC: 1802 AN: 5895

Middle Eastern (MID) AF: 0.218 AC: 47 AN: 216

European-Non Finnish (NFE) AF: 0.233 AC: 12319 AN: 52977

Other (OTH) AF: 0.345 AC: 518 AN: 1503

Alfa AF: 0.150 Hom.: 720

Bravo AF: 0.383

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.7
DANN	Benign	0.48
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs547425; hg19: chrX-112107745;