2-112842838-C-T

Variant names:

• chr2-112842838-C-T
• rs13032029
• ENST00000623243.1:n.2511C>T

Variant summary

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

The NR_197592.1(AMANZI):​n.3047C>T 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 0.379 in 152,124 control chromosomes in the GnomAD database, including 11,611 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 0.38 (11608 hom., cov: 32)
  • Exomes 𝑓: 0.35 (3 hom.)
• Consequence: AMANZI NR_197592.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.100
• Publications: 26 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=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.459 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.3047C>T		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.2511C>T		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000299339	ENST00000762706.1		n.405-42420C>T		intron	N/A
	ENSG00000299339	ENST00000762707.1		n.500-42420C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.379 AC: 57661 AN: 151946 Hom.: 11613 Cov.: 32

Gnomad AFR AF: 0.259

Gnomad AMI AF: 0.425

Gnomad AMR AF: 0.348

Gnomad ASJ AF: 0.399

Gnomad EAS AF: 0.475

Gnomad SAS AF: 0.277

Gnomad FIN AF: 0.389

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.457

Gnomad OTH AF: 0.387

GnomAD4 exome AF: 0.350 AC: 21 AN: 60 Hom.: 3 Cov.: 0 AF XY: 0.345 AC XY: 20 AN XY: 58

African (AFR) AC: 0 AN: 0

American (AMR) AF: 0.00 AC: 0 AN: 2

Ashkenazi Jewish (ASJ) AF: 0.500 AC: 1 AN: 2

East Asian (EAS) AF: 0.500 AC: 1 AN: 2

South Asian (SAS) AF: 0.500 AC: 1 AN: 2

European-Finnish (FIN) AF: 0.375 AC: 6 AN: 16

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.375 AC: 12 AN: 32

Other (OTH) AF: 0.00 AC: 0 AN: 4

GnomAD4 genome AF: 0.379 AC: 57656 AN: 152064 Hom.: 11608 Cov.: 32 AF XY: 0.376 AC XY: 27963 AN XY: 74334

African (AFR) AF: 0.259 AC: 10725 AN: 41480

American (AMR) AF: 0.347 AC: 5304 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.399 AC: 1387 AN: 3472

East Asian (EAS) AF: 0.475 AC: 2455 AN: 5168

South Asian (SAS) AF: 0.277 AC: 1336 AN: 4828

European-Finnish (FIN) AF: 0.389 AC: 4113 AN: 10570

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.457 AC: 31036 AN: 67944

Other (OTH) AF: 0.382 AC: 808 AN: 2114

Alfa AF: 0.389 Hom.: 2303

Bravo AF: 0.375

Asia WGS AF: 0.330 AC: 1145 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	2.2
DANN	Benign	0.53
PhyloP100		-0.10

Splicing

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

Other links and lift over

dbSNP: rs13032029; hg19: chr2-113600415;