rs55798477

Variant names:

• chr2-112841950-A-G
• rs55798477
• ENST00000623243.1:n.1623A>G

Variant summary

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

The ENST00000623243.1(ENSG00000280228):​n.1623A>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 0.151 in 152,218 control chromosomes in the GnomAD database, including 2,165 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 0.15 (2165 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000280228 ENST00000623243.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0870

Genes affected

ENSG00000280228 (HGNC:55634):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.206 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.1623A>G		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.151 AC: 23042 AN: 152100 Hom.: 2165 Cov.: 32

Gnomad AFR AF: 0.0501

Gnomad AMI AF: 0.309

Gnomad AMR AF: 0.137

Gnomad ASJ AF: 0.252

Gnomad EAS AF: 0.0461

Gnomad SAS AF: 0.127

Gnomad FIN AF: 0.206

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.209

Gnomad OTH AF: 0.172

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 4 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome AF: 0.151 AC: 23038 AN: 152218 Hom.: 2165 Cov.: 32 AF XY: 0.149 AC XY: 11068 AN XY: 74402

Gnomad4 AFR AF: 0.0500

Gnomad4 AMR AF: 0.137

Gnomad4 ASJ AF: 0.252

Gnomad4 EAS AF: 0.0460

Gnomad4 SAS AF: 0.128

Gnomad4 FIN AF: 0.206

Gnomad4 NFE AF: 0.209

Gnomad4 OTH AF: 0.171

Alfa AF: 0.179 Hom.: 343

Bravo AF: 0.141

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.7
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs55798477; hg19: chr2-113599527;