2-122846942-T-G

Variant names:

• chr2-122846942-T-G
• rs296036
• ENST00000657880.2:n.888+23125T>G

Variant summary

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

The ENST00000657880.2(ENSG00000286481):​n.888+23125T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.825 in 152,002 control chromosomes in the GnomAD database, including 51,747 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 0.82 (51747 hom., cov: 31)
• Consequence: ENSG00000286481 ENST00000657880.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.506
• Publications: 3 publications found

Genes affected

ENSG00000286481 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.875 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000657880.2. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000286481	ENST00000657880.2		n.888+23125T>G		intron	N/A
	ENSG00000286481	ENST00000687364.1		n.147+23125T>G		intron	N/A
	ENSG00000286481	ENST00000770504.1		n.428+23125T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.825 AC: 125250 AN: 151884 Hom.: 51696 Cov.: 31

Gnomad AFR AF: 0.850

Gnomad AMI AF: 0.749

Gnomad AMR AF: 0.809

Gnomad ASJ AF: 0.810

Gnomad EAS AF: 0.809

Gnomad SAS AF: 0.898

Gnomad FIN AF: 0.807

Gnomad MID AF: 0.851

Gnomad NFE AF: 0.813

Gnomad OTH AF: 0.826

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

GnomAD4 genome AF: 0.825 AC: 125358 AN: 152002 Hom.: 51747 Cov.: 31 AF XY: 0.825 AC XY: 61279 AN XY: 74298

African (AFR) AF: 0.850 AC: 35247 AN: 41464

American (AMR) AF: 0.809 AC: 12362 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.810 AC: 2810 AN: 3468

East Asian (EAS) AF: 0.808 AC: 4162 AN: 5150

South Asian (SAS) AF: 0.898 AC: 4323 AN: 4816

European-Finnish (FIN) AF: 0.807 AC: 8519 AN: 10562

Middle Eastern (MID) AF: 0.847 AC: 249 AN: 294

European-Non Finnish (NFE) AF: 0.813 AC: 55257 AN: 67942

Other (OTH) AF: 0.826 AC: 1747 AN: 2114

Alfa AF: 0.761 Hom.: 2506

Bravo AF: 0.825

Asia WGS AF: 0.878 AC: 3051 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.49
DANN	Benign	0.31
PhyloP100		-0.51

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs296036;

hg19: chr2-123604518;