rs4848306

Variant names:

• chr2-112840530-G-A
• rs4848306
• ENST00000623243.1:n.203G>A

Your query was ambiguous. Multiple possible variants found:

• chr2-112840530-G-A
• chr2-112840530-G-C

Variant summary

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

The NR_197592.1(AMANZI):​n.739G>A 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 0.39 in 152,724 control chromosomes in the GnomAD database, including 12,092 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 0.39 (12029 hom., cov: 32)
  • Exomes 𝑓: 0.42 (63 hom.)
• Consequence: AMANZI NR_197592.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.757
• Publications: 72 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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.476 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.739G>A		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.203G>A		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000299339	ENST00000762706.1		n.405-44728G>A		intron	N/A
	ENSG00000299339	ENST00000762707.1		n.500-44728G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.390 AC: 59312 AN: 151890 Hom.: 12036 Cov.: 32

Gnomad AFR AF: 0.298

Gnomad AMI AF: 0.423

Gnomad AMR AF: 0.349

Gnomad ASJ AF: 0.400

Gnomad EAS AF: 0.491

Gnomad SAS AF: 0.277

Gnomad FIN AF: 0.389

Gnomad MID AF: 0.328

Gnomad NFE AF: 0.456

Gnomad OTH AF: 0.394

GnomAD4 exome AF: 0.420 AC: 300 AN: 714 Hom.: 63 Cov.: 0 AF XY: 0.398 AC XY: 149 AN XY: 374

African (AFR) AF: 0.286 AC: 4 AN: 14

American (AMR) AF: 0.167 AC: 2 AN: 12

Ashkenazi Jewish (ASJ) AF: 0.438 AC: 7 AN: 16

East Asian (EAS) AF: 0.400 AC: 40 AN: 100

South Asian (SAS) AF: 0.00 AC: 0 AN: 4

European-Finnish (FIN) AF: 0.392 AC: 69 AN: 176

Middle Eastern (MID) AF: 0.500 AC: 1 AN: 2

European-Non Finnish (NFE) AF: 0.467 AC: 168 AN: 360

Other (OTH) AF: 0.300 AC: 9 AN: 30

GnomAD4 genome AF: 0.390 AC: 59304 AN: 152010 Hom.: 12029 Cov.: 32 AF XY: 0.387 AC XY: 28756 AN XY: 74308

African (AFR) AF: 0.297 AC: 12323 AN: 41442

American (AMR) AF: 0.348 AC: 5325 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.400 AC: 1385 AN: 3466

East Asian (EAS) AF: 0.492 AC: 2534 AN: 5154

South Asian (SAS) AF: 0.277 AC: 1336 AN: 4826

European-Finnish (FIN) AF: 0.389 AC: 4105 AN: 10554

Middle Eastern (MID) AF: 0.349 AC: 102 AN: 292

European-Non Finnish (NFE) AF: 0.456 AC: 30990 AN: 67978

Other (OTH) AF: 0.389 AC: 820 AN: 2110

Alfa AF: 0.432 Hom.: 20974

Bravo AF: 0.388

Asia WGS AF: 0.335 AC: 1164 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.43
DANN	Benign	0.77
PhyloP100		-0.76

Splicing

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

Other links and lift over

dbSNP: rs4848306; hg19: chr2-113598107;