rs7217422

Positions:

• chr17-45153098-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000589950.1(HEXIM2-AS1):​n.51-2179C>G variant causes a intron, non coding transcript 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 ENST00000589950.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.500

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HEXIM2-AS1	ENST00000589950.1	n.51-2179C>G		intron_variant, non_coding_transcript_variant		4
HEXIM2-AS1	ENST00000452741.2	n.242-2179C>G		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.142

Gnomad4 AMR AF: 0.147

Gnomad4 ASJ AF: 0.227

Gnomad4 EAS AF: 0.101

Gnomad4 SAS AF: 0.105

Gnomad4 FIN AF: 0.150

Gnomad4 NFE AF: 0.163

Gnomad4 OTH AF: 0.173

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7217422; hg19: chr17-43230465;