chrX-15611318-T-C

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000285602 (HGNC:):

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ACE2-DT	NR_126564.1	n.101+8337T>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285602	ENST00000649243.1	n.357-10304A>G		intron_variant	Intron 5 of 19			ENSP00000497489.1
ACE2-DT	ENST00000421585.1	n.101+8337T>C		intron_variant	Intron 1 of 1	2

Frequencies

GnomAD3 genomes AF: 0.239 AC: 26093 AN: 109398 Hom.: 2549 Cov.: 22 AF XY: 0.242 AC XY: 7793 AN XY: 32268

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

Gnomad4 AFR AF: 0.0982

Gnomad4 AMR AF: 0.271

Gnomad4 ASJ AF: 0.221

Gnomad4 EAS AF: 0.428

Gnomad4 SAS AF: 0.223

Gnomad4 FIN AF: 0.331

Gnomad4 NFE AF: 0.287

Gnomad4 OTH AF: 0.260

Alfa AF: 0.285 Hom.: 8391

Bravo AF: 0.233

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2097723; hg19: chrX-15629441;