2-122732606-C-T

Variant names:

• chr2-122732606-C-T
• rs13000913
• ENST00000657880.2:n.825-91148C>T

Variant summary

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

The ENST00000657880.2(ENSG00000286481):​n.825-91148C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.14 in 152,008 control chromosomes in the GnomAD database, including 1,671 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 0.14 (1671 hom., cov: 31)
• Consequence: ENSG00000286481 ENST00000657880.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26
• Publications: 1 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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.287 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.825-91148C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.140 AC: 21337 AN: 151890 Hom.: 1671 Cov.: 31

Gnomad AFR AF: 0.181

Gnomad AMI AF: 0.262

Gnomad AMR AF: 0.152

Gnomad ASJ AF: 0.0926

Gnomad EAS AF: 0.299

Gnomad SAS AF: 0.184

Gnomad FIN AF: 0.125

Gnomad MID AF: 0.121

Gnomad NFE AF: 0.102

Gnomad OTH AF: 0.136

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

GnomAD4 genome AF: 0.140 AC: 21355 AN: 152008 Hom.: 1671 Cov.: 31 AF XY: 0.145 AC XY: 10760 AN XY: 74270

African (AFR) AF: 0.181 AC: 7486 AN: 41450

American (AMR) AF: 0.152 AC: 2322 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.0926 AC: 321 AN: 3466

East Asian (EAS) AF: 0.300 AC: 1537 AN: 5130

South Asian (SAS) AF: 0.183 AC: 884 AN: 4820

European-Finnish (FIN) AF: 0.125 AC: 1326 AN: 10578

Middle Eastern (MID) AF: 0.127 AC: 37 AN: 292

European-Non Finnish (NFE) AF: 0.102 AC: 6913 AN: 67988

Other (OTH) AF: 0.138 AC: 291 AN: 2108

Alfa AF: 0.0692 Hom.: 76

Bravo AF: 0.146

Asia WGS AF: 0.253 AC: 878 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.38
DANN	Benign	0.72
PhyloP100		-1.3

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: rs13000913;

hg19: chr2-123490182;