ENST00000657880.2:n.824+54565G>A

Variant names:

• chr2-122587484-G-A
• rs1304771
• ENST00000657880.2:n.824+54565G>A

Variant summary

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

The ENST00000657880.2(ENSG00000286481):​n.824+54565G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.703 in 151,964 control chromosomes in the GnomAD database, including 37,873 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 0.70 (37873 hom., cov: 31)
• Consequence: ENSG00000286481 ENST00000657880.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.923
• 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=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.791 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.824+54565G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.703 AC: 106732 AN: 151846 Hom.: 37832 Cov.: 31

Gnomad AFR AF: 0.798

Gnomad AMI AF: 0.623

Gnomad AMR AF: 0.683

Gnomad ASJ AF: 0.591

Gnomad EAS AF: 0.651

Gnomad SAS AF: 0.507

Gnomad FIN AF: 0.733

Gnomad MID AF: 0.656

Gnomad NFE AF: 0.670

Gnomad OTH AF: 0.698

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

GnomAD4 genome AF: 0.703 AC: 106823 AN: 151964 Hom.: 37873 Cov.: 31 AF XY: 0.703 AC XY: 52206 AN XY: 74288

African (AFR) AF: 0.798 AC: 33079 AN: 41450

American (AMR) AF: 0.683 AC: 10417 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.591 AC: 2048 AN: 3468

East Asian (EAS) AF: 0.652 AC: 3352 AN: 5142

South Asian (SAS) AF: 0.506 AC: 2438 AN: 4816

European-Finnish (FIN) AF: 0.733 AC: 7764 AN: 10586

Middle Eastern (MID) AF: 0.658 AC: 192 AN: 292

European-Non Finnish (NFE) AF: 0.670 AC: 45503 AN: 67942

Other (OTH) AF: 0.696 AC: 1464 AN: 2104

Alfa AF: 0.687 Hom.: 6278

Bravo AF: 0.708

Asia WGS AF: 0.610 AC: 2124 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.96
DANN	Benign	0.32
PhyloP100		-0.92

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: rs1304771;

hg19: chr2-123345060;