rs17174152

Variant names:

• chrX-71183294-T-C
• rs17174152
• ENST00000664514.4:n.1323A>G

Variant summary

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

The ENST00000664514.4(ENSG00000228427):​n.1323A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.101 in 111,984 control chromosomes in the GnomAD database, including 770 homozygotes. There are 3,188 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 0.10 (770 hom., 3188 hem., cov: 23)
• Consequence: ENSG00000228427 ENST00000664514.4 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.465
• Publications: 0 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=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.235 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107985688	XR_001755878.2	n.*88A>G		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000228427	ENST00000664514.4	n.1323A>G		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000228427	ENST00000740246.1	n.346+617A>G		intron_variant	Intron 2 of 4
ENSG00000228427	ENST00000740247.1	n.367+617A>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.101 AC: 11300 AN: 111931 Hom.: 767 Cov.: 23

Gnomad AFR AF: 0.240

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0849

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.0920

Gnomad SAS AF: 0.0481

Gnomad FIN AF: 0.0442

Gnomad MID AF: 0.0875

Gnomad NFE AF: 0.0355

Gnomad OTH AF: 0.0861

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

GnomAD4 genome AF: 0.101 AC: 11319 AN: 111984 Hom.: 770 Cov.: 23 AF XY: 0.0933 AC XY: 3188 AN XY: 34184

African (AFR) AF: 0.240 AC: 7373 AN: 30725

American (AMR) AF: 0.0851 AC: 901 AN: 10586

Ashkenazi Jewish (ASJ) AF: 0.103 AC: 274 AN: 2649

East Asian (EAS) AF: 0.0917 AC: 326 AN: 3556

South Asian (SAS) AF: 0.0467 AC: 126 AN: 2696

European-Finnish (FIN) AF: 0.0442 AC: 272 AN: 6148

Middle Eastern (MID) AF: 0.0872 AC: 19 AN: 218

European-Non Finnish (NFE) AF: 0.0355 AC: 1890 AN: 53183

Other (OTH) AF: 0.0896 AC: 138 AN: 1540

Alfa AF: 0.0735 Hom.: 459

Bravo AF: 0.110

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.55
DANN	Benign	0.64
PhyloP100		-0.47

Splicing

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

Other links and lift over

dbSNP: rs17174152; hg19: chrX-70403144;