rs7217422

Variant names:

• chr17-45153098-G-C
• rs7217422
• ENST00000452741.3:n.258-2179C>G

Variant summary

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

The ENST00000452741.3(HEXIM2-AS1):​n.258-2179C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.153 in 151,830 control chromosomes in the GnomAD database, including 1,747 homozygotes. 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 (1747 hom., cov: 30)
• Consequence: HEXIM2-AS1 ENST00000452741.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.500
• Publications: 5 publications found

Genes affected

HEXIM2-AS1 (HGNC:55857): (HEXIM2 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.47).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.161 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HEXIM2-AS1	NR_186788.1	n.79-2179C>G		intron_variant	Intron 1 of 1
HEXIM2-AS1	NR_186789.1	n.242-2179C>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HEXIM2-AS1	ENST00000452741.3	n.258-2179C>G		intron_variant	Intron 2 of 2	3
HEXIM2-AS1	ENST00000589950.2	n.79-2179C>G		intron_variant	Intron 1 of 1	4
HEXIM2-AS1	ENST00000837780.1	n.93-2179C>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.153 AC: 23183 AN: 151712 Hom.: 1745 Cov.: 30

Gnomad AFR AF: 0.141

Gnomad AMI AF: 0.202

Gnomad AMR AF: 0.147

Gnomad ASJ AF: 0.227

Gnomad EAS AF: 0.101

Gnomad SAS AF: 0.105

Gnomad FIN AF: 0.150

Gnomad MID AF: 0.226

Gnomad NFE AF: 0.163

Gnomad OTH AF: 0.175

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

GnomAD4 genome AF: 0.153 AC: 23196 AN: 151830 Hom.: 1747 Cov.: 30 AF XY: 0.151 AC XY: 11180 AN XY: 74168

African (AFR) AF: 0.142 AC: 5854 AN: 41370

American (AMR) AF: 0.147 AC: 2243 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.227 AC: 788 AN: 3468

East Asian (EAS) AF: 0.101 AC: 523 AN: 5168

South Asian (SAS) AF: 0.105 AC: 506 AN: 4820

European-Finnish (FIN) AF: 0.150 AC: 1573 AN: 10482

Middle Eastern (MID) AF: 0.233 AC: 68 AN: 292

European-Non Finnish (NFE) AF: 0.163 AC: 11094 AN: 67964

Other (OTH) AF: 0.173 AC: 365 AN: 2106

Alfa AF: 0.0845 Hom.: 118

Bravo AF: 0.151

Asia WGS AF: 0.0900 AC: 312 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.47
CADD	Benign	7.8
DANN	Benign	0.94
PhyloP100		-0.50

Splicing

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

Other links and lift over

dbSNP: rs7217422; hg19: chr17-43230465;