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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000664514.4. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000228427	ENST00000664514.4		n.156C>G		non_coding_transcript_exon	Exon 1 of 2
	ENSG00000228427	ENST00000450860.1	TSL:3	n.-177C>G		upstream_gene	N/A
	ENSG00000228427	ENST00000652147.3		n.-87C>G		upstream_gene	N/A

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 v4.9

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;