rs2229302

Variant names:

• chr17-48543040-G-A
• rs2229302
• NM_002145.4:c.*28C>T

Your query was ambiguous. Multiple possible variants found:

• chr17-48543040-G-A
• chr17-48543040-G-T

Variant summary

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

The NM_002145.4(HOXB2):​c.*28C>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 0.18 in 1,532,648 control chromosomes in the GnomAD database, including 26,203 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 (2080 hom., cov: 31)
  • Exomes 𝑓: 0.18 (24123 hom.)
• Consequence: HOXB2 NM_002145.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.289
• Publications: 33 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=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.193 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.*28C>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.*28C>T		3_prime_UTR	Exon 2 of 2	ENSP00000331741.4
	HOXB2	ENST00000504772.3	TSL:3	n.107C>T		non_coding_transcript_exon	Exon 1 of 2
	HOXB-AS1	ENST00000717337.1		n.39G>A		non_coding_transcript_exon	Exon 1 of 2

Frequencies

GnomAD3 genomes AF: 0.156 AC: 23747 AN: 152002 Hom.: 2078 Cov.: 31

Gnomad AFR AF: 0.0810

Gnomad AMI AF: 0.296

Gnomad AMR AF: 0.156

Gnomad ASJ AF: 0.183

Gnomad EAS AF: 0.0871

Gnomad SAS AF: 0.129

Gnomad FIN AF: 0.222

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.195

Gnomad OTH AF: 0.167

GnomAD2 exomes AF: 0.163 AC: 31811 AN: 195640 AF XY: 0.165

Gnomad AFR exome AF: 0.0771

Gnomad AMR exome AF: 0.134

Gnomad ASJ exome AF: 0.185

Gnomad EAS exome AF: 0.0802

Gnomad FIN exome AF: 0.222

Gnomad NFE exome AF: 0.192

Gnomad OTH exome AF: 0.174

GnomAD4 exome AF: 0.182 AC: 251816 AN: 1380528 Hom.: 24123 Cov.: 29 AF XY: 0.181 AC XY: 123044 AN XY: 680812

African (AFR) AF: 0.0758 AC: 2288 AN: 30198

American (AMR) AF: 0.138 AC: 4476 AN: 32386

Ashkenazi Jewish (ASJ) AF: 0.192 AC: 4198 AN: 21872

East Asian (EAS) AF: 0.0546 AC: 2044 AN: 37444

South Asian (SAS) AF: 0.120 AC: 8905 AN: 74410

European-Finnish (FIN) AF: 0.221 AC: 11335 AN: 51234

Middle Eastern (MID) AF: 0.141 AC: 760 AN: 5396

European-Non Finnish (NFE) AF: 0.194 AC: 207933 AN: 1070902

Other (OTH) AF: 0.174 AC: 9877 AN: 56686

GnomAD4 genome AF: 0.156 AC: 23754 AN: 152120 Hom.: 2080 Cov.: 31 AF XY: 0.157 AC XY: 11661 AN XY: 74370

African (AFR) AF: 0.0811 AC: 3368 AN: 41520

American (AMR) AF: 0.156 AC: 2384 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.183 AC: 634 AN: 3466

East Asian (EAS) AF: 0.0868 AC: 450 AN: 5186

South Asian (SAS) AF: 0.130 AC: 626 AN: 4810

European-Finnish (FIN) AF: 0.222 AC: 2352 AN: 10580

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.195 AC: 13273 AN: 67958

Other (OTH) AF: 0.165 AC: 347 AN: 2108

Alfa AF: 0.169 Hom.: 2355

Bravo AF: 0.148

Asia WGS AF: 0.132 AC: 460 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.3
DANN	Benign	0.74
PhyloP100		-0.29
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		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: rs2229302; hg19: chr17-46620402;