11-34232613-A-G

Variant summary

Our verdict is Benign. Variant got -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

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=-0.94).
• 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/exons	MANE	UniProt
ABTB2	NM_145804.3	c.884-27923T>C		intron_variant		ENST00000435224.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ABTB2	ENST00000435224.3	c.884-27923T>C		intron_variant		1	NM_145804.3	P1
ABTB2	ENST00000530814.1	n.71+9862T>C		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.828

Gnomad4 AMR AF: 0.943

Gnomad4 ASJ AF: 0.948

Gnomad4 EAS AF: 0.868

Gnomad4 SAS AF: 0.921

Gnomad4 FIN AF: 0.996

Gnomad4 NFE AF: 0.983

Gnomad4 OTH AF: 0.926

Alfa AF: 0.951 Hom.: 11649

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

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: rs2955948; hg19: chr11-34254160; COSMIC: COSV54389960;