chr11-34232136-C-T

Variant names:

• chr11-34232136-C-T
• rs2926467
• NM_145804.3:c.884-27446G>A

Variant summary

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

The NM_145804.3(ABTB2):​c.884-27446G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.693 in 152,048 control chromosomes in the GnomAD database, including 36,616 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 0.69 (36616 hom., cov: 32)
• Consequence: ABTB2 NM_145804.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.102
• Publications: 3 publications found

Genes affected

ABTB2 (HGNC:23842): (ankyrin repeat and BTB domain containing 2) Predicted to enable protein heterodimerization activity. Predicted to act upstream of or within cellular response to toxic substance. [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=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.7 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_145804.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ABTB2	NM_145804.3	MANE Select	c.884-27446G>A		intron	N/A	NP_665803.2	Q8N961-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ABTB2	ENST00000435224.3	TSL:1 MANE Select	c.884-27446G>A		intron	N/A	ENSP00000410157.2	Q8N961-1
	ABTB2	ENST00000868012.1		c.884-34598G>A		intron	N/A	ENSP00000538071.1
	ABTB2	ENST00000530814.1	TSL:4	n.71+10339G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.693 AC: 105346 AN: 151930 Hom.: 36592 Cov.: 32

Gnomad AFR AF: 0.706

Gnomad AMI AF: 0.527

Gnomad AMR AF: 0.653

Gnomad ASJ AF: 0.738

Gnomad EAS AF: 0.591

Gnomad SAS AF: 0.662

Gnomad FIN AF: 0.722

Gnomad MID AF: 0.799

Gnomad NFE AF: 0.700

Gnomad OTH AF: 0.688

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

GnomAD4 genome AF: 0.693 AC: 105411 AN: 152048 Hom.: 36616 Cov.: 32 AF XY: 0.692 AC XY: 51432 AN XY: 74322

African (AFR) AF: 0.707 AC: 29277 AN: 41438

American (AMR) AF: 0.652 AC: 9956 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.738 AC: 2561 AN: 3470

East Asian (EAS) AF: 0.591 AC: 3055 AN: 5170

South Asian (SAS) AF: 0.662 AC: 3185 AN: 4812

European-Finnish (FIN) AF: 0.722 AC: 7651 AN: 10592

Middle Eastern (MID) AF: 0.801 AC: 234 AN: 292

European-Non Finnish (NFE) AF: 0.700 AC: 47556 AN: 67972

Other (OTH) AF: 0.689 AC: 1456 AN: 2112

Alfa AF: 0.685 Hom.: 15570

Bravo AF: 0.687

Asia WGS AF: 0.629 AC: 2189 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	2.1
DANN	Benign	0.77
PhyloP100		-0.10
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: rs2926467; hg19: chr11-34253683;