2-88016274-C-T

Variant names:

• chr2-88016274-C-T
• rs12714207
• ENST00000827621.1:n.277G>A

Variant summary

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

The ENST00000827621.1(ENSG00000307645):​n.277G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.627 in 152,012 control chromosomes in the GnomAD database, including 30,272 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 0.63 (30271 hom., cov: 33)
  • Exomes 𝑓: 1.0 (1 hom.)
• Consequence: ENSG00000307645 ENST00000827621.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.124
• Publications: 17 publications found

Genes affected

ENSG00000307645 (HGNC:):

RNU2-63P (HGNC:48556): (RNA, U2 small nuclear 63, pseudogene)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.804 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RNU2-63P	NR_199865.1	n.*84G>A		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000307645	ENST00000827621.1	n.277G>A		non_coding_transcript_exon_variant	Exon 1 of 2
ENSG00000307645	ENST00000827625.1	n.274G>A		non_coding_transcript_exon_variant	Exon 1 of 1
ENSG00000307645	ENST00000827620.1	n.145+362G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.627 AC: 95245 AN: 151892 Hom.: 30259 Cov.: 33

Gnomad AFR AF: 0.523

Gnomad AMI AF: 0.798

Gnomad AMR AF: 0.617

Gnomad ASJ AF: 0.701

Gnomad EAS AF: 0.825

Gnomad SAS AF: 0.749

Gnomad FIN AF: 0.636

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.661

Gnomad OTH AF: 0.631

GnomAD4 exome AF: 1.00 AC: 2 AN: 2 Hom.: 1 AF XY: 1.00 AC XY: 2 AN XY: 2

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 1.00 AC: 2 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.627 AC: 95294 AN: 152010 Hom.: 30271 Cov.: 33 AF XY: 0.628 AC XY: 46689 AN XY: 74292

African (AFR) AF: 0.523 AC: 21656 AN: 41430

American (AMR) AF: 0.616 AC: 9421 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.701 AC: 2432 AN: 3470

East Asian (EAS) AF: 0.824 AC: 4249 AN: 5154

South Asian (SAS) AF: 0.749 AC: 3613 AN: 4826

European-Finnish (FIN) AF: 0.636 AC: 6715 AN: 10560

Middle Eastern (MID) AF: 0.622 AC: 183 AN: 294

European-Non Finnish (NFE) AF: 0.661 AC: 44961 AN: 67974

Other (OTH) AF: 0.635 AC: 1338 AN: 2106

Alfa AF: 0.613 Hom.: 4374

Bravo AF: 0.616

Asia WGS AF: 0.770 AC: 2680 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	0.94
DANN	Benign	0.18
PhyloP100		0.12
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs12714207; hg19: chr2-88315793;