2-122533446-C-T

Variant names:

• chr2-122533446-C-T
• rs1527243
• ENST00000657880.1:n.773+527C>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000657880.1(ENSG00000286481):​n.773+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 ENST00000657880.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.85

Genes affected

ENSG00000286481 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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	ENST00000657880.1	n.773+527C>T		intron_variant	Intron 4 of 8

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

Gnomad4 AFR AF: 0.359

Gnomad4 AMR AF: 0.699

Gnomad4 ASJ AF: 0.848

Gnomad4 EAS AF: 0.829

Gnomad4 SAS AF: 0.777

Gnomad4 FIN AF: 0.861

Gnomad4 NFE AF: 0.849

Gnomad4 OTH AF: 0.727

Alfa AF: 0.821 Hom.: 95775

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

Splicing

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

Publications

LitVar

Other links and lift over

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