chr11-34232613-A-G

Variant names:

• chr11-34232613-A-G
• rs2955948
• NM_145804.3:c.884-27923T>C

Variant summary

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

The NM_145804.3(ABTB2):​c.884-27923T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.93 in 152,126 control chromosomes in the GnomAD database, including 66,165 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 0.93 (66165 hom., cov: 29)
• Consequence: ABTB2 NM_145804.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.200
• 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=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ABTB2	NM_145804.3	c.884-27923T>C		intron_variant	Intron 1 of 16	ENST00000435224.3	NP_665803.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ABTB2	ENST00000435224.3	c.884-27923T>C		intron_variant	Intron 1 of 16	1	NM_145804.3	ENSP00000410157.2
ABTB2	ENST00000530814.1	n.71+9862T>C		intron_variant	Intron 1 of 3	4

Frequencies

GnomAD3 genomes AF: 0.930 AC: 141401 AN: 152008 Hom.: 66127 Cov.: 29

Gnomad AFR AF: 0.828

Gnomad AMI AF: 0.999

Gnomad AMR AF: 0.943

Gnomad ASJ AF: 0.948

Gnomad EAS AF: 0.868

Gnomad SAS AF: 0.921

Gnomad FIN AF: 0.996

Gnomad MID AF: 0.940

Gnomad NFE AF: 0.983

Gnomad OTH AF: 0.925

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

GnomAD4 genome AF: 0.930 AC: 141492 AN: 152126 Hom.: 66165 Cov.: 29 AF XY: 0.931 AC XY: 69241 AN XY: 74394

African (AFR) AF: 0.828 AC: 34302 AN: 41444

American (AMR) AF: 0.943 AC: 14422 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.948 AC: 3290 AN: 3470

East Asian (EAS) AF: 0.868 AC: 4496 AN: 5178

South Asian (SAS) AF: 0.921 AC: 4425 AN: 4806

European-Finnish (FIN) AF: 0.996 AC: 10555 AN: 10602

Middle Eastern (MID) AF: 0.942 AC: 277 AN: 294

European-Non Finnish (NFE) AF: 0.983 AC: 66860 AN: 68020

Other (OTH) AF: 0.926 AC: 1954 AN: 2110

Alfa AF: 0.949 Hom.: 11938

Bravo AF: 0.920

Asia WGS AF: 0.901 AC: 3133 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.4
DANN	Benign	0.65
PhyloP100		0.20
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: rs2955948; hg19: chr11-34254160; COSMIC: COSV54389960;