rs8070447

Variant names:

• chr17-45151932-A-C
• rs8070447
• NM_006460.3:c.*1662A>C

Your query was ambiguous. Multiple possible variants found:

• chr17-45151932-A-C
• chr17-45151932-A-G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 12 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
HEXIM1	NM_006460.3	c.*1662A>C		3_prime_UTR_variant	Exon 1 of 1	ENST00000332499.4	NP_006451.1
HEXIM2-AS1	NR_186788.1	n.79-1013T>G		intron_variant	Intron 1 of 1
HEXIM2-AS1	NR_186789.1	n.242-1013T>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HEXIM1	ENST00000332499.4	c.*1662A>C		3_prime_UTR_variant	Exon 1 of 1	6	NM_006460.3	ENSP00000328773.3

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

African (AFR) AF: 0.167 AC: 1 AN: 6

American (AMR) AF: 0.250 AC: 1 AN: 4

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.250 AC: 1 AN: 4

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.206 AC: 3019 AN: 14690

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2

European-Non Finnish (NFE) AF: 0.0833 AC: 7 AN: 84

Other (OTH) AF: 0.250 AC: 23 AN: 92

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

African (AFR) AF: 0.208 AC: 8638 AN: 41486

American (AMR) AF: 0.142 AC: 2176 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.100 AC: 347 AN: 3470

East Asian (EAS) AF: 0.342 AC: 1773 AN: 5178

South Asian (SAS) AF: 0.150 AC: 725 AN: 4830

European-Finnish (FIN) AF: 0.210 AC: 2219 AN: 10584

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.109 AC: 7405 AN: 68020

Other (OTH) AF: 0.136 AC: 287 AN: 2114

Alfa AF: 0.124 Hom.: 1125

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
PhyloP100		-0.56
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

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