ENST00000623243.1:n.1623A>G

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000623243.1(AMANZI):​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: AMANZI ENST00000623243.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0870
• Publications: 1 publications found

Genes affected

AMANZI (HGNC:55634):

ENSG00000299339 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000623243.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AMANZI	NR_197592.1		n.2159A>G		non_coding_transcript_exon	Exon 1 of 1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AMANZI	ENST00000623243.1	TSL:6	n.1623A>G		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000299339	ENST00000762706.1		n.405-43308A>G		intron	N/A
	ENSG00000299339	ENST00000762707.1		n.500-43308A>G		intron	N/A

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 2

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.0500 AC: 2080 AN: 41572

American (AMR) AF: 0.137 AC: 2093 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.252 AC: 873 AN: 3468

East Asian (EAS) AF: 0.0460 AC: 238 AN: 5176

South Asian (SAS) AF: 0.128 AC: 616 AN: 4828

European-Finnish (FIN) AF: 0.206 AC: 2181 AN: 10594

Middle Eastern (MID) AF: 0.306 AC: 90 AN: 294

European-Non Finnish (NFE) AF: 0.209 AC: 14225 AN: 67990

Other (OTH) AF: 0.171 AC: 361 AN: 2108

Alfa AF: 0.179 Hom.: 343

Bravo AF: 0.141

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.7
DANN	Benign	0.59
PhyloP100		0.087

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs55798477;

hg19: chr2-113599527;