rs8070447

chr17-45151932-A-Cchr17-45151932-A-G

Variant summary

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

The NM_006460.3(HEXIM1):c.*1662A>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.16 in 167,058 control chromosomes in the GnomAD database, including 2,438 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 0.16 (2106 hom., cov: 33)
  • Exomes 𝑓: 0.21 (332 hom.)
• Consequence: HEXIM1 NM_006460.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.556

Genes affected

HEXIM1 (HGNC:24953): (HEXIM P-TEFb complex subunit 1) Expression of this gene is induced by hexamethylene-bis-acetamide in vascular smooth muscle cells. This gene has no introns. [provided by RefSeq, Jul 2008]

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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.329 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HEXIM1	NM_006460.3	c.*1662A>C		3_prime_UTR_variant	1/1	ENST00000332499.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HEXIM1	ENST00000332499.4	c.*1662A>C		3_prime_UTR_variant	1/1		NM_006460.3	P1
HEXIM2-AS1	ENST00000589950.1	n.51-1013T>G		intron_variant, non_coding_transcript_variant		4
HEXIM2-AS1	ENST00000452741.2	n.242-1013T>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.156 AC: 23670 AN: 152058 Hom.: 2098 Cov.: 33

Gnomad AFR AF: 0.208

Gnomad AMI AF: 0.121

Gnomad AMR AF: 0.142

Gnomad ASJ AF: 0.100

Gnomad EAS AF: 0.342

Gnomad SAS AF: 0.150

Gnomad FIN AF: 0.210

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.109

Gnomad OTH AF: 0.134

GnomAD4 exome AF: 0.205 AC: 3052 AN: 14882 Hom.: 332 Cov.: 0 AF XY: 0.204 AC XY: 1439 AN XY: 7062

Gnomad4 AFR exome AF: 0.167

Gnomad4 AMR exome AF: 0.250

Gnomad4 EAS exome AF: 0.250

Gnomad4 FIN exome AF: 0.206

Gnomad4 NFE exome AF: 0.0833

Gnomad4 OTH exome AF: 0.250

GnomAD4 genome AF: 0.156 AC: 23704 AN: 152176 Hom.: 2106 Cov.: 33 AF XY: 0.161 AC XY: 11963 AN XY: 74394

Gnomad4 AFR AF: 0.208

Gnomad4 AMR AF: 0.142

Gnomad4 ASJ AF: 0.100

Gnomad4 EAS AF: 0.342

Gnomad4 SAS AF: 0.150

Gnomad4 FIN AF: 0.210

Gnomad4 NFE AF: 0.109

Gnomad4 OTH AF: 0.136

Alfa AF: 0.125 Hom.: 899

Bravo AF: 0.156

Asia WGS AF: 0.250 AC: 869 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	2.0
Dann	Benign	0.83

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs8070447; hg19: chr17-43229299; COSMIC: COSV60176770; COSMIC: COSV60176770;