11-34262314-C-T

Variant names:

• chr11-34262314-C-T
• rs2611145
• NM_145804.3:c.884-57624G>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.884-57624G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.479 in 151,888 control chromosomes in the GnomAD database, including 17,890 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 0.48 (17890 hom., cov: 31)
• Consequence: ABTB2 NM_145804.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.53
• Publications: 6 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=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.567 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ABTB2	NM_145804.3	c.884-57624G>A		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.884-57624G>A		intron_variant	Intron 1 of 16	1	NM_145804.3	ENSP00000410157.2

Frequencies

GnomAD3 genomes AF: 0.479 AC: 72764 AN: 151772 Hom.: 17899 Cov.: 31

Gnomad AFR AF: 0.356

Gnomad AMI AF: 0.638

Gnomad AMR AF: 0.491

Gnomad ASJ AF: 0.495

Gnomad EAS AF: 0.408

Gnomad SAS AF: 0.585

Gnomad FIN AF: 0.470

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.548

Gnomad OTH AF: 0.485

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

GnomAD4 genome AF: 0.479 AC: 72759 AN: 151888 Hom.: 17890 Cov.: 31 AF XY: 0.477 AC XY: 35402 AN XY: 74222

African (AFR) AF: 0.356 AC: 14741 AN: 41418

American (AMR) AF: 0.490 AC: 7478 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.495 AC: 1716 AN: 3468

East Asian (EAS) AF: 0.409 AC: 2110 AN: 5164

South Asian (SAS) AF: 0.585 AC: 2811 AN: 4806

European-Finnish (FIN) AF: 0.470 AC: 4953 AN: 10546

Middle Eastern (MID) AF: 0.548 AC: 161 AN: 294

European-Non Finnish (NFE) AF: 0.548 AC: 37201 AN: 67934

Other (OTH) AF: 0.480 AC: 1006 AN: 2096

Alfa AF: 0.527 Hom.: 40167

Bravo AF: 0.471

Asia WGS AF: 0.454 AC: 1579 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.0
DANN	Benign	0.60
PhyloP100		1.5
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: rs2611145; hg19: chr11-34283861;