rs1538779

chr1-47848164-T-Cchr1-47848164-T-G

Variant summary

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

The NM_001194986.2(TRABD2B):c.667-46545A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.297 in 152,164 control chromosomes in the GnomAD database, including 6,844 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 0.30 (6844 hom., cov: 33)
• Consequence: TRABD2B NM_001194986.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0780

Genes affected

TRABD2B (HGNC:44200): (TraB domain containing 2B) Enables Wnt-protein binding activity and metalloendopeptidase activity. Involved in several processes, including negative regulation of Wnt signaling pathway; positive regulation of protein oxidation; and positive regulation of protein-containing complex assembly. Is integral component of organelle membrane and integral component of plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.446 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TRABD2B	NM_001194986.2	c.667-46545A>G		intron_variant		ENST00000606738.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TRABD2B	ENST00000606738.3	c.667-46545A>G		intron_variant		1	NM_001194986.2	P1
TRABD2B	ENST00000435576.2	n.180-46545A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.297 AC: 45100 AN: 152046 Hom.: 6840 Cov.: 33

Gnomad AFR AF: 0.261

Gnomad AMI AF: 0.258

Gnomad AMR AF: 0.255

Gnomad ASJ AF: 0.333

Gnomad EAS AF: 0.461

Gnomad SAS AF: 0.248

Gnomad FIN AF: 0.367

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.306

Gnomad OTH AF: 0.301

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.297 AC: 45148 AN: 152164 Hom.: 6844 Cov.: 33 AF XY: 0.297 AC XY: 22093 AN XY: 74406

Gnomad4 AFR AF: 0.261

Gnomad4 AMR AF: 0.255

Gnomad4 ASJ AF: 0.333

Gnomad4 EAS AF: 0.461

Gnomad4 SAS AF: 0.249

Gnomad4 FIN AF: 0.367

Gnomad4 NFE AF: 0.306

Gnomad4 OTH AF: 0.305

Alfa AF: 0.300 Hom.: 2132

Bravo AF: 0.288

Asia WGS AF: 0.359 AC: 1244 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	1.8
Dann	Benign	0.73

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: rs1538779; hg19: chr1-48313836;