dbSNP rs1042815: HOXB2:c.*142C>T (chr17-48542926-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_002145.4(HOXB2):c.*142C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.585 in 510,568 control chromosomes in the GnomAD database, including 91,279 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 0.52 ( 22840 hom., cov: 31)

Exomes 𝑓: 0.61 ( 68439 hom. )

Consequence

HOXB2
NM_002145.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.15

Publications

46 publications found

Variant links:

Genes affected

HOXB2 (HGNC:5113): (homeobox B2) This gene is a member of the Antp homeobox family and encodes a nuclear protein with a homeobox DNA-binding domain. It is included in a cluster of homeobox B genes located on chromosome 17. The encoded protein functions as a sequence-specific transcription factor that is involved in development. Increased expression of this gene is associated with pancreatic cancer. [provided by RefSeq, Jul 2008]

HOXB2 links:

HOXB-AS1 (HGNC:43744): (HOXB cluster antisense RNA 1)

HOXB-AS1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.81).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.682 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HOXB2	NM_002145.4 link	c.*142C>T		3_prime_UTR_variant	Exon 2 of 2	ENST00000330070.6	NP_002136.1	P14652
HOXB2	XM_005257275.5 link	c.*142C>T		3_prime_UTR_variant	Exon 2 of 2		XP_005257332.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
HOXB2	ENST00000330070.6 link	c.*142C>T	3_prime_UTR_variant	Exon 2 of 2	1	NM_002145.4	ENSP00000331741.4	P14652
HOXB2	ENST00000504772.3 link	n.192+29C>T	intron_variant	Intron 1 of 1	3
HOXB-AS1	ENST00000717337.1 link	n.-76G>A	upstream_gene_variant
HOXB2	ENST00000571287.1 link	n.*233C>T	downstream_gene_variant		3

Frequencies

GnomAD3 genomes

AF:

0.524

AC:

79604

AN:

151868

Hom.:

22819

Cov.:

show subpopulations

Gnomad AFR

AF:

0.264

Gnomad AMI

AF:

0.554

Gnomad AMR

AF:

0.660

Gnomad ASJ

AF:

0.641

Gnomad EAS

AF:

0.668

Gnomad SAS

AF:

0.702

Gnomad FIN

AF:

0.582

Gnomad MID

AF:

0.639

Gnomad NFE

AF:

0.611

Gnomad OTH

AF:

0.568

GnomAD4 exome

AF:

0.611

AC:

218996

AN:

358580

Hom.:

68439

Cov.:

AF XY:

0.614

AC XY:

112312

AN XY:

183052

show subpopulations

African (AFR)

AF:

0.256

AC:

2333

AN:

9108

American (AMR)

AF:

0.692

AC:

7520

AN:

10860

Ashkenazi Jewish (ASJ)

AF:

0.632

AC:

6656

AN:

10524

East Asian (EAS)

AF:

0.722

AC:

17972

AN:

24906

South Asian (SAS)

AF:

0.702

AC:

9396

AN:

13380

European-Finnish (FIN)

AF:

0.588

AC:

21008

AN:

35706

Middle Eastern (MID)

AF:

0.656

AC:

1694

AN:

2582

European-Non Finnish (NFE)

AF:

0.607

AC:

140162

AN:

230866

Other (OTH)

AF:

0.594

AC:

12255

AN:

20648

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

4267

8533

12800

17066

21333

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.524

AC:

79651

AN:

151988

Hom.:

22840

Cov.:

AF XY:

0.529

AC XY:

39312

AN XY:

74288

show subpopulations

African (AFR)

AF:

0.264

AC:

10946

AN:

41440

American (AMR)

AF:

0.661

AC:

10097

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.641

AC:

2225

AN:

3472

East Asian (EAS)

AF:

0.668

AC:

3451

AN:

5166

South Asian (SAS)

AF:

0.701

AC:

3375

AN:

4812

European-Finnish (FIN)

AF:

0.582

AC:

6145

AN:

10554

Middle Eastern (MID)

AF:

0.650

AC:

191

AN:

294

European-Non Finnish (NFE)

AF:

0.611

AC:

41515

AN:

67956

Other (OTH)

AF:

0.571

AC:

1203

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

1768

3535

5303

7070

8838

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.587

Hom.:

47100

Bravo

AF:

0.516

Asia WGS

AF:

0.665

AC:

2315

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

(source)

DANN

Benign

0.79

PhyloP100

1.1

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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rs1042815

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over