2-122803120-T-C

Variant names:

• chr2-122803120-T-C
• rs294665
• ENST00000657880.2:n.825-20634T>C

Variant summary

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

The ENST00000657880.2(ENSG00000286481):​n.825-20634T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.842 in 152,186 control chromosomes in the GnomAD database, including 54,110 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 0.84 (54110 hom., cov: 33)
• Consequence: ENSG00000286481 ENST00000657880.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.360
• Publications: 7 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 = 0.877 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000286481	ENST00000657880.2		n.825-20634T>C		intron	N/A
	ENSG00000286481	ENST00000687364.1		n.84-20634T>C		intron	N/A
	ENSG00000286481	ENST00000770504.1		n.365-20634T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.842 AC: 128109 AN: 152068 Hom.: 54063 Cov.: 33

Gnomad AFR AF: 0.878

Gnomad AMI AF: 0.796

Gnomad AMR AF: 0.816

Gnomad ASJ AF: 0.804

Gnomad EAS AF: 0.821

Gnomad SAS AF: 0.899

Gnomad FIN AF: 0.818

Gnomad MID AF: 0.877

Gnomad NFE AF: 0.831

Gnomad OTH AF: 0.835

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

GnomAD4 genome AF: 0.842 AC: 128215 AN: 152186 Hom.: 54110 Cov.: 33 AF XY: 0.842 AC XY: 62669 AN XY: 74412

African (AFR) AF: 0.878 AC: 36443 AN: 41510

American (AMR) AF: 0.816 AC: 12477 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.804 AC: 2788 AN: 3468

East Asian (EAS) AF: 0.820 AC: 4227 AN: 5158

South Asian (SAS) AF: 0.900 AC: 4345 AN: 4830

European-Finnish (FIN) AF: 0.818 AC: 8674 AN: 10598

Middle Eastern (MID) AF: 0.874 AC: 257 AN: 294

European-Non Finnish (NFE) AF: 0.831 AC: 56514 AN: 68016

Other (OTH) AF: 0.835 AC: 1767 AN: 2116

Alfa AF: 0.828 Hom.: 12860

Bravo AF: 0.844

Asia WGS AF: 0.887 AC: 3081 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	0.77
DANN	Benign	0.66
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs294665; hg19: chr2-123560696;