rs7892772

Variant names:

• chrX-71198352-G-C
• rs7892772
• ENST00000664514.4:n.156C>G

Variant summary

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

The ENST00000664514.4(ENSG00000228427):​n.156C>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 0.145 in 110,512 control chromosomes in the GnomAD database, including 1,220 homozygotes. There are 4,492 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 0.15 (1220 hom., 4492 hem., cov: 22)
• Consequence: ENSG00000228427 ENST00000664514.4 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.527
• 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.276 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107985688	XR_001755878.2	n.-159C>G		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000228427	ENST00000664514.4	n.156C>G		non_coding_transcript_exon_variant	Exon 1 of 2
ENSG00000228427	ENST00000450860.1	n.-177C>G		upstream_gene_variant		3
ENSG00000228427	ENST00000652147.3	n.-87C>G		upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.145 AC: 16034 AN: 110459 Hom.: 1215 Cov.: 22

Gnomad AFR AF: 0.281

Gnomad AMI AF: 0.108

Gnomad AMR AF: 0.116

Gnomad ASJ AF: 0.150

Gnomad EAS AF: 0.0870

Gnomad SAS AF: 0.0627

Gnomad FIN AF: 0.110

Gnomad MID AF: 0.102

Gnomad NFE AF: 0.0863

Gnomad OTH AF: 0.121

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

GnomAD4 genome AF: 0.145 AC: 16057 AN: 110512 Hom.: 1220 Cov.: 22 AF XY: 0.137 AC XY: 4492 AN XY: 32864

African (AFR) AF: 0.281 AC: 8514 AN: 30293

American (AMR) AF: 0.116 AC: 1192 AN: 10294

Ashkenazi Jewish (ASJ) AF: 0.150 AC: 394 AN: 2628

East Asian (EAS) AF: 0.0870 AC: 306 AN: 3516

South Asian (SAS) AF: 0.0606 AC: 162 AN: 2672

European-Finnish (FIN) AF: 0.110 AC: 642 AN: 5846

Middle Eastern (MID) AF: 0.102 AC: 22 AN: 216

European-Non Finnish (NFE) AF: 0.0863 AC: 4563 AN: 52868

Other (OTH) AF: 0.126 AC: 189 AN: 1502

Alfa AF: 0.117 Hom.: 645

Bravo AF: 0.154

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	9.1
DANN	Benign	0.64
PhyloP100		0.53

Splicing

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

Other links and lift over

dbSNP: rs7892772; hg19: chrX-70418202;