11-34346870-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_145804.3(ABTB2):c.883+9831G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.154 in 152,144 control chromosomes in the GnomAD database, including 3,157 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 0.15 (3157 hom., cov: 32)
• Consequence: ABTB2 NM_145804.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0540

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.345 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ABTB2	NM_145804.3	c.883+9831G>A		intron_variant		ENST00000435224.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ABTB2	ENST00000435224.3	c.883+9831G>A		intron_variant		1	NM_145804.3	P1

Frequencies

GnomAD3 genomes AF: 0.154 AC: 23410 AN: 152028 Hom.: 3154 Cov.: 32

Gnomad AFR AF: 0.350

Gnomad AMI AF: 0.0297

Gnomad AMR AF: 0.106

Gnomad ASJ AF: 0.0858

Gnomad EAS AF: 0.354

Gnomad SAS AF: 0.0364

Gnomad FIN AF: 0.0389

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.0617

Gnomad OTH AF: 0.149

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

GnomAD4 genome AF: 0.154 AC: 23437 AN: 152144 Hom.: 3157 Cov.: 32 AF XY: 0.151 AC XY: 11249 AN XY: 74386

Gnomad4 AFR AF: 0.350

Gnomad4 AMR AF: 0.105

Gnomad4 ASJ AF: 0.0858

Gnomad4 EAS AF: 0.354

Gnomad4 SAS AF: 0.0366

Gnomad4 FIN AF: 0.0389

Gnomad4 NFE AF: 0.0617

Gnomad4 OTH AF: 0.149

Alfa AF: 0.0215 Hom.: 16

Bravo AF: 0.172

Asia WGS AF: 0.199 AC: 692 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
Cadd	Benign	5.7
Dann	Benign	0.84

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

Publications

LitVar

Other links and lift over

dbSNP: rs2001176; hg19: chr11-34368417;