chr2-112842989-C-G

Variant names:

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

Variant summary

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

The NR_197592.1(AMANZI):​n.3198C>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: AMANZI NR_197592.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0970
• Publications: 0 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=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.132 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_197592.1. 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.3198C>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.2662C>G		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000299339	ENST00000762706.1		n.405-42269C>G		intron	N/A
	ENSG00000299339	ENST00000762707.1		n.500-42269C>G		intron	N/A

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

African (AFR) AF: 1.00 AC: 2 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 0.250 AC: 1 AN: 4

East Asian (EAS) AF: 0.00 AC: 0 AN: 6

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: 0.0897 AC: 7 AN: 78

Other (OTH) AF: 0.00 AC: 0 AN: 8

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

African (AFR) AF: 0.0548 AC: 2277 AN: 41558

American (AMR) AF: 0.0420 AC: 643 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.116 AC: 402 AN: 3470

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5180

South Asian (SAS) AF: 0.141 AC: 679 AN: 4820

European-Finnish (FIN) AF: 0.0698 AC: 741 AN: 10614

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.0614 AC: 4174 AN: 68030

Other (OTH) AF: 0.0666 AC: 141 AN: 2116

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.0
DANN	Benign	0.44
PhyloP100		-0.097

Splicing

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

Other links and lift over

dbSNP: rs56100202; hg19: chr2-113600566;