rs4670779

Positions:

• chr2-37817201-C-T

Variant summary

Our verdict is Benign. Variant got -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: ENST00000456500.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.124

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000456500.1	n.287C>T		non_coding_transcript_exon_variant	1/1

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

Gnomad4 AFR exome AF: 0.0595

Gnomad4 AMR exome AF: 0.340

Gnomad4 ASJ exome AF: 0.265

Gnomad4 EAS exome AF: 0.249

Gnomad4 SAS exome AF: 0.292

Gnomad4 FIN exome AF: 0.270

Gnomad4 NFE exome AF: 0.314

Gnomad4 OTH exome AF: 0.281

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

Gnomad4 AFR AF: 0.0607

Gnomad4 AMR AF: 0.310

Gnomad4 ASJ AF: 0.263

Gnomad4 EAS AF: 0.237

Gnomad4 SAS AF: 0.284

Gnomad4 FIN AF: 0.257

Gnomad4 NFE AF: 0.314

Gnomad4 OTH AF: 0.229

Alfa AF: 0.301 Hom.: 11444

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4670779; hg19: chr2-38044344;