rs56100202

Variant names:

• chr2-112842989-C-G
• rs56100202
• ENST00000623243.1:n.2662C>G

Your query was ambiguous. Multiple possible variants found:

• 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:55634):

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000280228	ENST00000623243.1	n.2662C>G		non_coding_transcript_exon_variant	Exon 1 of 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;