X-15611318-T-C

Variant names:

• chrX-15611318-T-C
• rs2097723
• ENST00000649243.1:n.357-10304A>G

Variant summary

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

The ENST00000649243.1(ENSG00000285602):​n.357-10304A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.239 in 109,442 control chromosomes in the GnomAD database, including 2,549 homozygotes. There are 7,799 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 0.24 (2549 hom., 7799 hem., cov: 22)
• Consequence: ENSG00000285602 ENST00000649243.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.863
• Publications: 11 publications found

Genes affected

ENSG00000285602 (HGNC:):

ACE2-DT (HGNC:56255): (ACE2 divergent transcript)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.41 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000649243.1. 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
	ACE2-DT	NR_126564.1		n.101+8337T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000285602	ENST00000649243.1		n.357-10304A>G		intron	N/A	ENSP00000497489.1	A0A3B3IT09
	ACE2-DT	ENST00000421585.2	TSL:2	n.124+8337T>C		intron	N/A
	ACE2-DT	ENST00000742836.1		n.114-2783T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.239 AC: 26093 AN: 109398 Hom.: 2549 Cov.: 22

Gnomad AFR AF: 0.0983

Gnomad AMI AF: 0.301

Gnomad AMR AF: 0.271

Gnomad ASJ AF: 0.221

Gnomad EAS AF: 0.428

Gnomad SAS AF: 0.223

Gnomad FIN AF: 0.331

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.287

Gnomad OTH AF: 0.257

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

GnomAD4 genome AF: 0.239 AC: 26103 AN: 109442 Hom.: 2549 Cov.: 22 AF XY: 0.241 AC XY: 7799 AN XY: 32320

African (AFR) AF: 0.0982 AC: 2877 AN: 29297

American (AMR) AF: 0.271 AC: 2815 AN: 10373

Ashkenazi Jewish (ASJ) AF: 0.221 AC: 583 AN: 2638

East Asian (EAS) AF: 0.428 AC: 1496 AN: 3493

South Asian (SAS) AF: 0.223 AC: 583 AN: 2614

European-Finnish (FIN) AF: 0.331 AC: 1940 AN: 5864

Middle Eastern (MID) AF: 0.236 AC: 50 AN: 212

European-Non Finnish (NFE) AF: 0.287 AC: 15166 AN: 52778

Other (OTH) AF: 0.260 AC: 391 AN: 1503

Alfa AF: 0.268 Hom.: 10835

Bravo AF: 0.233

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.56
DANN	Benign	0.36
PhyloP100		-0.86

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: rs2097723;

hg19: chrX-15629441;