rs55798477

chr2-112841950-A-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: ENST00000623243.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0870

Genes affected

(HGNC:):

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000623243.1	n.1623A>G		non_coding_transcript_exon_variant	1/1

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;