rs11211631

Variant names:

• chr1-47918069-A-C
• rs11211631
• NM_001194986.2:c.666+75965T>G

Your query was ambiguous. Multiple possible variants found:

• chr1-47918069-A-C
• chr1-47918069-A-T

Variant summary

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

The NM_001194986.2(TRABD2B):​c.666+75965T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.46 in 152,118 control chromosomes in the GnomAD database, including 17,918 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 0.46 (17918 hom., cov: 33)
• Consequence: TRABD2B NM_001194986.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.639
• Publications: 4 publications found

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

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 = 0.581 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRABD2B	NM_001194986.2	c.666+75965T>G		intron_variant	Intron 2 of 6	ENST00000606738.3	NP_001181915.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRABD2B	ENST00000606738.3	c.666+75965T>G		intron_variant	Intron 2 of 6	1	NM_001194986.2	ENSP00000476820.1
TRABD2B	ENST00000435576.2	n.179+75965T>G		intron_variant	Intron 1 of 3	3

Frequencies

GnomAD3 genomes AF: 0.460 AC: 69954 AN: 152000 Hom.: 17914 Cov.: 33

Gnomad AFR AF: 0.232

Gnomad AMI AF: 0.560

Gnomad AMR AF: 0.444

Gnomad ASJ AF: 0.659

Gnomad EAS AF: 0.358

Gnomad SAS AF: 0.598

Gnomad FIN AF: 0.466

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.586

Gnomad OTH AF: 0.516

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

GnomAD4 genome AF: 0.460 AC: 69970 AN: 152118 Hom.: 17918 Cov.: 33 AF XY: 0.459 AC XY: 34145 AN XY: 74352

African (AFR) AF: 0.232 AC: 9628 AN: 41526

American (AMR) AF: 0.443 AC: 6765 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.659 AC: 2287 AN: 3468

East Asian (EAS) AF: 0.359 AC: 1853 AN: 5162

South Asian (SAS) AF: 0.599 AC: 2888 AN: 4822

European-Finnish (FIN) AF: 0.466 AC: 4922 AN: 10564

Middle Eastern (MID) AF: 0.616 AC: 181 AN: 294

European-Non Finnish (NFE) AF: 0.586 AC: 39840 AN: 67978

Other (OTH) AF: 0.518 AC: 1095 AN: 2114

Alfa AF: 0.420 Hom.: 2007

Bravo AF: 0.443

Asia WGS AF: 0.454 AC: 1582 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	4.0
DANN	Benign	0.85
PhyloP100		0.64
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: rs11211631; hg19: chr1-48383741;