rs4848306

chr2-112840530-G-Achr2-112840530-G-C

Variant summary

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

The ENST00000623243.1(ENSG00000280228):n.203G>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 0.39 in 152,724 control chromosomes in the GnomAD database, including 12,092 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 0.39 (12029 hom., cov: 32)
  • Exomes 𝑓: 0.42 (63 hom.)
• Consequence: ENST00000623243.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.757

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.476 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
	ENST00000623243.1	n.203G>A		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.390 AC: 59312 AN: 151890 Hom.: 12036 Cov.: 32

Gnomad AFR AF: 0.298

Gnomad AMI AF: 0.423

Gnomad AMR AF: 0.349

Gnomad ASJ AF: 0.400

Gnomad EAS AF: 0.491

Gnomad SAS AF: 0.277

Gnomad FIN AF: 0.389

Gnomad MID AF: 0.328

Gnomad NFE AF: 0.456

Gnomad OTH AF: 0.394

GnomAD4 exome AF: 0.420 AC: 300 AN: 714 Hom.: 63 Cov.: 0 AF XY: 0.398 AC XY: 149 AN XY: 374

Gnomad4 AFR exome AF: 0.286

Gnomad4 AMR exome AF: 0.167

Gnomad4 ASJ exome AF: 0.438

Gnomad4 EAS exome AF: 0.400

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.392

Gnomad4 NFE exome AF: 0.467

Gnomad4 OTH exome AF: 0.300

GnomAD4 genome AF: 0.390 AC: 59304 AN: 152010 Hom.: 12029 Cov.: 32 AF XY: 0.387 AC XY: 28756 AN XY: 74308

Gnomad4 AFR AF: 0.297

Gnomad4 AMR AF: 0.348

Gnomad4 ASJ AF: 0.400

Gnomad4 EAS AF: 0.492

Gnomad4 SAS AF: 0.277

Gnomad4 FIN AF: 0.389

Gnomad4 NFE AF: 0.456

Gnomad4 OTH AF: 0.389

Alfa AF: 0.415 Hom.: 1743

Bravo AF: 0.388

Asia WGS AF: 0.335 AC: 1164 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	0.43
Dann	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4848306; hg19: chr2-113598107;