chrX-15621438-T-G

Variant names:

• chrX-15621438-T-G
• rs1548474
• ENST00000649243.1:n.356+18124A>C

Variant summary

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

The ENST00000649243.1(ENSG00000285602):​n.356+18124A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.295 in 111,165 control chromosomes in the GnomAD database, including 3,514 homozygotes. There are 9,693 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 0.29 (3514 hom., 9693 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000285602 ENST00000649243.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.784
• Publications: 8 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=-0.75).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.408 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.528T>G		non_coding_transcript_exon	Exon 2 of 2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000285602	ENST00000649243.1		n.356+18124A>C		intron	N/A	ENSP00000497489.1	A0A3B3IT09
	ACE2-DT	ENST00000421585.2	TSL:2	n.551T>G		non_coding_transcript_exon	Exon 2 of 2
	ACE2-DT	ENST00000742836.1		n.741T>G		non_coding_transcript_exon	Exon 3 of 3

Frequencies

GnomAD3 genomes AF: 0.295 AC: 32754 AN: 111113 Hom.: 3512 Cov.: 23

Gnomad AFR AF: 0.295

Gnomad AMI AF: 0.306

Gnomad AMR AF: 0.294

Gnomad ASJ AF: 0.224

Gnomad EAS AF: 0.425

Gnomad SAS AF: 0.221

Gnomad FIN AF: 0.334

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.289

Gnomad OTH AF: 0.304

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.295 AC: 32778 AN: 111165 Hom.: 3514 Cov.: 23 AF XY: 0.290 AC XY: 9693 AN XY: 33401

African (AFR) AF: 0.295 AC: 9048 AN: 30635

American (AMR) AF: 0.294 AC: 3072 AN: 10448

Ashkenazi Jewish (ASJ) AF: 0.224 AC: 589 AN: 2630

East Asian (EAS) AF: 0.426 AC: 1502 AN: 3528

South Asian (SAS) AF: 0.220 AC: 591 AN: 2681

European-Finnish (FIN) AF: 0.334 AC: 1952 AN: 5847

Middle Eastern (MID) AF: 0.249 AC: 53 AN: 213

European-Non Finnish (NFE) AF: 0.289 AC: 15299 AN: 52992

Other (OTH) AF: 0.307 AC: 464 AN: 1512

Alfa AF: 0.285 Hom.: 28731

Bravo AF: 0.300

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	7.3
DANN	Benign	0.83
PhyloP100		0.78

Splicing

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

Other links and lift over

dbSNP: rs1548474; hg19: chrX-15639561;