2-122638301-C-T

Variant names:

• chr2-122638301-C-T
• rs13400652
• ENST00000657880.2:n.824+105382C>T

Variant summary

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

The ENST00000657880.2(ENSG00000286481):​n.824+105382C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.412 in 151,780 control chromosomes in the GnomAD database, including 14,186 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 0.41 (14186 hom., cov: 31)
• Consequence: ENSG00000286481 ENST00000657880.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.66
• 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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.51 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286481	ENST00000657880.2	n.824+105382C>T		intron_variant	Intron 4 of 8

Frequencies

GnomAD3 genomes AF: 0.412 AC: 62517 AN: 151662 Hom.: 14183 Cov.: 31

Gnomad AFR AF: 0.212

Gnomad AMI AF: 0.403

Gnomad AMR AF: 0.462

Gnomad ASJ AF: 0.357

Gnomad EAS AF: 0.389

Gnomad SAS AF: 0.411

Gnomad FIN AF: 0.495

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.515

Gnomad OTH AF: 0.418

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

GnomAD4 genome AF: 0.412 AC: 62528 AN: 151780 Hom.: 14186 Cov.: 31 AF XY: 0.410 AC XY: 30400 AN XY: 74120

African (AFR) AF: 0.212 AC: 8788 AN: 41412

American (AMR) AF: 0.462 AC: 7050 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.357 AC: 1237 AN: 3466

East Asian (EAS) AF: 0.390 AC: 2003 AN: 5142

South Asian (SAS) AF: 0.411 AC: 1976 AN: 4812

European-Finnish (FIN) AF: 0.495 AC: 5181 AN: 10476

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.515 AC: 34939 AN: 67906

Other (OTH) AF: 0.420 AC: 884 AN: 2104

Alfa AF: 0.475 Hom.: 22160

Bravo AF: 0.401

Asia WGS AF: 0.381 AC: 1325 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.092
DANN	Benign	0.46
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs13400652; hg19: chr2-123395877;