rs1042815

Variant names:

• chr17-48542926-G-A
• rs1042815
• NM_002145.4:c.*142C>T

Your query was ambiguous. Multiple possible variants found:

• chr17-48542926-G-A
• chr17-48542926-G-C

Variant summary

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

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.15
• Publications: 46 publications found

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]

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

ACMG classification

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002145.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HOXB2	NM_002145.4	MANE Select	c.*142C>T		3_prime_UTR	Exon 2 of 2	NP_002136.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HOXB2	ENST00000330070.6	TSL:1 MANE Select	c.*142C>T		3_prime_UTR	Exon 2 of 2	ENSP00000331741.4
	HOXB2	ENST00000504772.3	TSL:3	n.192+29C>T		intron	N/A
	HOXB-AS1	ENST00000717337.1		n.-76G>A		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.524 AC: 79604 AN: 151868 Hom.: 22819 Cov.: 31

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.: 5 AF XY: 0.614 AC XY: 112312 AN XY: 183052

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

GnomAD4 genome AF: 0.524 AC: 79651 AN: 151988 Hom.: 22840 Cov.: 31 AF XY: 0.529 AC XY: 39312 AN XY: 74288

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

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	12
DANN	Benign	0.79
PhyloP100		1.1
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: rs1042815; hg19: chr17-46620288; COSMIC: COSV57486188; COSMIC: COSV57486188;