2-122533446-C-T

Variant names:

• chr2-122533446-C-T
• rs1527243
• ENST00000657880.2:n.824+527C>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+527C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.697 in 152,002 control chromosomes in the GnomAD database, including 40,353 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 (40353 hom., cov: 31)
• Consequence: ENSG00000286481 ENST00000657880.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.85
• Publications: 11 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=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.843 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+527C>T		intron_variant	Intron 4 of 8
ENSG00000286481	ENST00000819387.1	n.69+527C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.697 AC: 105875 AN: 151884 Hom.: 40345 Cov.: 31

Gnomad AFR AF: 0.360

Gnomad AMI AF: 0.859

Gnomad AMR AF: 0.698

Gnomad ASJ AF: 0.848

Gnomad EAS AF: 0.829

Gnomad SAS AF: 0.776

Gnomad FIN AF: 0.861

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.849

Gnomad OTH AF: 0.729

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

GnomAD4 genome AF: 0.697 AC: 105907 AN: 152002 Hom.: 40353 Cov.: 31 AF XY: 0.700 AC XY: 51990 AN XY: 74302

African (AFR) AF: 0.359 AC: 14884 AN: 41406

American (AMR) AF: 0.699 AC: 10663 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.848 AC: 2938 AN: 3466

East Asian (EAS) AF: 0.829 AC: 4273 AN: 5152

South Asian (SAS) AF: 0.777 AC: 3735 AN: 4810

European-Finnish (FIN) AF: 0.861 AC: 9112 AN: 10584

Middle Eastern (MID) AF: 0.796 AC: 234 AN: 294

European-Non Finnish (NFE) AF: 0.849 AC: 57751 AN: 68004

Other (OTH) AF: 0.727 AC: 1534 AN: 2110

Alfa AF: 0.798 Hom.: 202983

Bravo AF: 0.668

Asia WGS AF: 0.731 AC: 2542 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.11
DANN	Benign	0.46
PhyloP100		-2.8

Splicing

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

Other links and lift over

dbSNP: rs1527243; hg19: chr2-123291022; COSMIC: COSV50192767;