2-155563980-A-G

Position:

• chr2-155563980-A-G

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000286679 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LOC107985953	XR_001739746.3	n.252+19651A>G		intron_variant
LOC107985953	XR_001739747.3	n.68-24837A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000286679	ENST00000653496.1	n.260+3438A>G		intron_variant
ENSG00000286679	ENST00000655023.1	n.328+3438A>G		intron_variant
ENSG00000286679	ENST00000656573.1	n.214+3438A>G		intron_variant

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

Gnomad4 AFR AF: 0.482

Gnomad4 AMR AF: 0.736

Gnomad4 ASJ AF: 0.702

Gnomad4 EAS AF: 0.823

Gnomad4 SAS AF: 0.708

Gnomad4 FIN AF: 0.660

Gnomad4 NFE AF: 0.670

Gnomad4 OTH AF: 0.638

Alfa AF: 0.666 Hom.: 44611

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs278865; hg19: chr2-156420492;