ENST00000456500.1:n.287C>T

Variant names:

• chr2-37817201-C-T
• rs4670779
• ENST00000456500.1:n.287C>T

Variant summary

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

The ENST00000456500.1(ENSG00000225402):​n.287C>T 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 0.285 in 816,014 control chromosomes in the GnomAD database, including 35,292 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 0.24 (5283 hom., cov: 32)
  • Exomes 𝑓: 0.30 (30009 hom.)
• Consequence: ENSG00000225402 ENST00000456500.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.124
• Publications: 8 publications found

Genes affected

ENSG00000225402 (HGNC:):

CDC42EP3-AS1 (HGNC:56370): (CDC42EP3 antisense RNA 1)

PIRAT1 (HGNC:37459): (PU.1 (SPI1) induced regulator of S100A8 and S100A9 alarmin transcription 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.61).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.31 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC344382		n.37817201C>T		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000225402	ENST00000456500.1	n.287C>T		non_coding_transcript_exon_variant	Exon 1 of 1	6
CDC42EP3-AS1	ENST00000751609.1	n.516-49583C>T		intron_variant	Intron 4 of 5
CDC42EP3-AS1	ENST00000751628.1	n.47-49583C>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.236 AC: 35830 AN: 152006 Hom.: 5281 Cov.: 32

Gnomad AFR AF: 0.0609

Gnomad AMI AF: 0.453

Gnomad AMR AF: 0.311

Gnomad ASJ AF: 0.263

Gnomad EAS AF: 0.237

Gnomad SAS AF: 0.284

Gnomad FIN AF: 0.257

Gnomad MID AF: 0.328

Gnomad NFE AF: 0.314

Gnomad OTH AF: 0.228

GnomAD4 exome AF: 0.296 AC: 196622 AN: 663886 Hom.: 30009 Cov.: 7 AF XY: 0.297 AC XY: 106804 AN XY: 359492

African (AFR) AF: 0.0595 AC: 1086 AN: 18242

American (AMR) AF: 0.340 AC: 14862 AN: 43724

Ashkenazi Jewish (ASJ) AF: 0.265 AC: 5610 AN: 21132

East Asian (EAS) AF: 0.249 AC: 9021 AN: 36244

South Asian (SAS) AF: 0.292 AC: 20555 AN: 70324

European-Finnish (FIN) AF: 0.270 AC: 14334 AN: 53106

Middle Eastern (MID) AF: 0.282 AC: 909 AN: 3218

European-Non Finnish (NFE) AF: 0.314 AC: 120664 AN: 383786

Other (OTH) AF: 0.281 AC: 9581 AN: 34110

GnomAD4 genome AF: 0.236 AC: 35827 AN: 152128 Hom.: 5283 Cov.: 32 AF XY: 0.234 AC XY: 17394 AN XY: 74364

African (AFR) AF: 0.0607 AC: 2518 AN: 41510

American (AMR) AF: 0.310 AC: 4743 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.263 AC: 911 AN: 3470

East Asian (EAS) AF: 0.237 AC: 1224 AN: 5168

South Asian (SAS) AF: 0.284 AC: 1370 AN: 4824

European-Finnish (FIN) AF: 0.257 AC: 2724 AN: 10592

Middle Eastern (MID) AF: 0.336 AC: 98 AN: 292

European-Non Finnish (NFE) AF: 0.314 AC: 21343 AN: 67970

Other (OTH) AF: 0.229 AC: 484 AN: 2110

Alfa AF: 0.282 Hom.: 16802

Bravo AF: 0.231

Asia WGS AF: 0.267 AC: 927 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	3.2
DANN	Benign	0.27
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs4670779; hg19: chr2-38044344;