ENST00000653496.1:n.260+3438A>G

Variant names:

• chr2-155563980-A-G
• rs278865
• ENST00000653496.1:n.260+3438A>G

Variant summary

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

The ENST00000653496.1(ENSG00000286679):​n.260+3438A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.631 in 151,912 control chromosomes in the GnomAD database, including 30,996 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 0.63 (30996 hom., cov: 30)
• Consequence: ENSG00000286679 ENST00000653496.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.766
• Publications: 2 publications found

Genes affected

ENSG00000286679 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.802 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107985953	XR_001739746.3	n.252+19651A>G		intron_variant	Intron 3 of 5
LOC107985953	XR_001739747.3	n.68-24837A>G		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286679	ENST00000653496.1	n.260+3438A>G		intron_variant	Intron 3 of 6
ENSG00000286679	ENST00000655023.1	n.328+3438A>G		intron_variant	Intron 4 of 6
ENSG00000286679	ENST00000656573.1	n.214+3438A>G		intron_variant	Intron 3 of 5

Frequencies

GnomAD3 genomes AF: 0.631 AC: 95817 AN: 151794 Hom.: 30991 Cov.: 30

Gnomad AFR AF: 0.482

Gnomad AMI AF: 0.643

Gnomad AMR AF: 0.736

Gnomad ASJ AF: 0.702

Gnomad EAS AF: 0.823

Gnomad SAS AF: 0.710

Gnomad FIN AF: 0.660

Gnomad MID AF: 0.685

Gnomad NFE AF: 0.669

Gnomad OTH AF: 0.639

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

GnomAD4 genome AF: 0.631 AC: 95861 AN: 151912 Hom.: 30996 Cov.: 30 AF XY: 0.636 AC XY: 47238 AN XY: 74238

African (AFR) AF: 0.482 AC: 19953 AN: 41402

American (AMR) AF: 0.736 AC: 11245 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.702 AC: 2434 AN: 3466

East Asian (EAS) AF: 0.823 AC: 4240 AN: 5152

South Asian (SAS) AF: 0.708 AC: 3418 AN: 4826

European-Finnish (FIN) AF: 0.660 AC: 6961 AN: 10542

Middle Eastern (MID) AF: 0.678 AC: 198 AN: 292

European-Non Finnish (NFE) AF: 0.670 AC: 45481 AN: 67928

Other (OTH) AF: 0.638 AC: 1347 AN: 2112

Alfa AF: 0.661 Hom.: 55829

Bravo AF: 0.627

Asia WGS AF: 0.748 AC: 2600 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.68
DANN	Benign	0.59
PhyloP100		-0.77

Splicing

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

Other links and lift over

dbSNP: rs278865; hg19: chr2-156420492;