rs56100202

Positions:

• chr2-112842989-C-G
• chr2-112842989-C-T

Variant summary

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

The ENST00000623243.1(ENSG00000280228):​n.2662C>G 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 0.0598 in 152,392 control chromosomes in the GnomAD database, including 313 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 0.060 (312 hom., cov: 32)
  • Exomes 𝑓: 0.10 (1 hom.)
• Consequence: ENSG00000280228 ENST00000623243.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0970

Genes affected

ENSG00000280228 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.132 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.112842989C>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000280228	ENST00000623243.1	n.2662C>G		non_coding_transcript_exon_variant	1/1	6

Frequencies

GnomAD3 genomes AF: 0.0598 AC: 9096 AN: 152174 Hom.: 311 Cov.: 32

Gnomad AFR AF: 0.0548

Gnomad AMI AF: 0.00658

Gnomad AMR AF: 0.0421

Gnomad ASJ AF: 0.116

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.0698

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.0613

Gnomad OTH AF: 0.0664

GnomAD4 exome AF: 0.100 AC: 10 AN: 100 Hom.: 1 Cov.: 0 AF XY: 0.116 AC XY: 10 AN XY: 86

Gnomad4 AFR exome AF: 1.00

Gnomad4 ASJ exome AF: 0.250

Gnomad4 EAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0897

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0598 AC: 9102 AN: 152292 Hom.: 312 Cov.: 32 AF XY: 0.0610 AC XY: 4539 AN XY: 74462

Gnomad4 AFR AF: 0.0548

Gnomad4 AMR AF: 0.0420

Gnomad4 ASJ AF: 0.116

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.141

Gnomad4 FIN AF: 0.0698

Gnomad4 NFE AF: 0.0614

Gnomad4 OTH AF: 0.0666

Alfa AF: 0.0256 Hom.: 13

Bravo AF: 0.0554

Asia WGS AF: 0.0780 AC: 270 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.0
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs56100202; hg19: chr2-113600566;