chr12-107357000-T-C

Variant names:

• chr12-107357000-T-C
• rs4964213
• NM_001018072.2:c.1135+36925T>C

Variant summary

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

The NM_001018072.2(ABTB3):​c.1135+36925T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.714 in 152,194 control chromosomes in the GnomAD database, including 39,571 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 0.71 (39571 hom., cov: 33)
• Consequence: ABTB3 NM_001018072.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.33
• Publications: 4 publications found

Genes affected

ABTB3 (HGNC:23844): (ankyrin repeat and BTB domain containing 3) Predicted to enable protein heterodimerization activity. Predicted to be involved in SMAD protein signal transduction. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000306026 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.849 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ABTB3	NM_001018072.2	c.1135+36925T>C		intron_variant	Intron 1 of 16	ENST00000280758.10	NP_001018082.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ABTB3	ENST00000280758.10	c.1135+36925T>C		intron_variant	Intron 1 of 16	5	NM_001018072.2	ENSP00000280758.5

Frequencies

GnomAD3 genomes AF: 0.714 AC: 108643 AN: 152076 Hom.: 39548 Cov.: 33

Gnomad AFR AF: 0.857

Gnomad AMI AF: 0.656

Gnomad AMR AF: 0.676

Gnomad ASJ AF: 0.725

Gnomad EAS AF: 0.554

Gnomad SAS AF: 0.763

Gnomad FIN AF: 0.655

Gnomad MID AF: 0.728

Gnomad NFE AF: 0.655

Gnomad OTH AF: 0.705

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

GnomAD4 genome AF: 0.714 AC: 108707 AN: 152194 Hom.: 39571 Cov.: 33 AF XY: 0.716 AC XY: 53258 AN XY: 74410

African (AFR) AF: 0.856 AC: 35575 AN: 41540

American (AMR) AF: 0.676 AC: 10336 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.725 AC: 2518 AN: 3472

East Asian (EAS) AF: 0.553 AC: 2858 AN: 5170

South Asian (SAS) AF: 0.763 AC: 3679 AN: 4822

European-Finnish (FIN) AF: 0.655 AC: 6938 AN: 10592

Middle Eastern (MID) AF: 0.738 AC: 217 AN: 294

European-Non Finnish (NFE) AF: 0.655 AC: 44509 AN: 67980

Other (OTH) AF: 0.700 AC: 1479 AN: 2114

Alfa AF: 0.674 Hom.: 59937

Bravo AF: 0.720

Asia WGS AF: 0.633 AC: 2202 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.56
DANN	Benign	0.65
PhyloP100		-1.3
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: rs4964213; hg19: chr12-107750777;