chr1-112521149-C-T

Position:

• chr1-112521149-C-T

Variant summary

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

The NM_024494.3(WNT2B):​c.*640C>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 0.186 in 152,868 control chromosomes in the GnomAD database, including 3,326 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 0.19 (3304 hom., cov: 31)
  • Exomes 𝑓: 0.20 (22 hom.)
• Consequence: WNT2B NM_024494.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.497

Genes affected

WNT2B (HGNC:12781): (Wnt family member 2B) This gene encodes a member of the wingless-type MMTV integration site (WNT) family of highly conserved, secreted signaling factors. WNT family members function in a variety of developmental processes including regulation of cell growth and differentiation and are characterized by a WNT-core domain. This gene may play a role in human development as well as carcinogenesis. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2014]

ST7L (HGNC:18441): (suppression of tumorigenicity 7 like) This gene was identified by its similarity to the ST7 tumor suppressor gene found in the chromosome 7q31 region. This gene is clustered in a tail-to-tail manner with the WNT2B gene in a chromosomal region known to be deleted and rearranged in a variety of cancers. Several transcript variants encoding many different isoforms have been described, but some have not been fully characterized. [provided by RefSeq, Feb 2011]

ST7L (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.443 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
WNT2B	NM_024494.3	c.*640C>T		3_prime_UTR_variant	5/5	ENST00000369684.5	NP_078613.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
WNT2B	ENST00000369684.5	c.*640C>T		3_prime_UTR_variant	5/5	1	NM_024494.3	ENSP00000358698.4
WNT2B	ENST00000369686.9	c.*640C>T		3_prime_UTR_variant	6/6	1		ENSP00000358700.4
WNT2B	ENST00000256640.9	c.*640C>T		3_prime_UTR_variant	5/5	2		ENSP00000256640.5

Frequencies

GnomAD3 genomes AF: 0.186 AC: 28293 AN: 151854 Hom.: 3302 Cov.: 31

Gnomad AFR AF: 0.0762

Gnomad AMI AF: 0.294

Gnomad AMR AF: 0.253

Gnomad ASJ AF: 0.258

Gnomad EAS AF: 0.458

Gnomad SAS AF: 0.209

Gnomad FIN AF: 0.296

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.194

Gnomad OTH AF: 0.184

GnomAD4 exome AF: 0.201 AC: 180 AN: 896 Hom.: 22 Cov.: 0 AF XY: 0.210 AC XY: 94 AN XY: 448

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.309

Gnomad4 SAS exome AF: 0.306

Gnomad4 FIN exome AF: 0.167

Gnomad4 NFE exome AF: 0.173

Gnomad4 OTH exome AF: 0.136

GnomAD4 genome AF: 0.186 AC: 28297 AN: 151972 Hom.: 3304 Cov.: 31 AF XY: 0.195 AC XY: 14473 AN XY: 74280

Gnomad4 AFR AF: 0.0761

Gnomad4 AMR AF: 0.254

Gnomad4 ASJ AF: 0.258

Gnomad4 EAS AF: 0.458

Gnomad4 SAS AF: 0.209

Gnomad4 FIN AF: 0.296

Gnomad4 NFE AF: 0.194

Gnomad4 OTH AF: 0.182

Alfa AF: 0.188 Hom.: 3196

Bravo AF: 0.184

Asia WGS AF: 0.312 AC: 1081 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.39
DANN	Benign	0.36

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: rs2273368; hg19: chr1-113063771;