rs12621220

Variant names:

• chr2-112840678-C-T
• rs12621220
• ENST00000623243.1:n.351C>T

Variant summary

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

The ENST00000623243.1(AMANZI):​n.351C>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 0.248 in 152,140 control chromosomes in the GnomAD database, including 5,486 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 0.25 (5485 hom., cov: 32)
  • Exomes 𝑓: 0.17 (1 hom.)
• Consequence: AMANZI ENST00000623243.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.80
• Publications: 25 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.391 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AMANZI	NR_197592.1	n.887C>T		non_coding_transcript_exon_variant	Exon 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AMANZI	ENST00000623243.1	n.351C>T		non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000299339	ENST00000762706.1	n.405-44580C>T		intron_variant	Intron 2 of 3
ENSG00000299339	ENST00000762707.1	n.500-44580C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.248 AC: 37671 AN: 151976 Hom.: 5465 Cov.: 32

Gnomad AFR AF: 0.108

Gnomad AMI AF: 0.258

Gnomad AMR AF: 0.398

Gnomad ASJ AF: 0.219

Gnomad EAS AF: 0.396

Gnomad SAS AF: 0.355

Gnomad FIN AF: 0.334

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.269

Gnomad OTH AF: 0.245

GnomAD4 exome AF: 0.174 AC: 8 AN: 46 Hom.: 1 Cov.: 0 AF XY: 0.192 AC XY: 5 AN XY: 26

African (AFR) AC: 0 AN: 0

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

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

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

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.227 AC: 5 AN: 22

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.100 AC: 2 AN: 20

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.248 AC: 37714 AN: 152094 Hom.: 5485 Cov.: 32 AF XY: 0.257 AC XY: 19098 AN XY: 74316

African (AFR) AF: 0.108 AC: 4464 AN: 41520

American (AMR) AF: 0.399 AC: 6099 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.219 AC: 760 AN: 3466

East Asian (EAS) AF: 0.396 AC: 2048 AN: 5174

South Asian (SAS) AF: 0.355 AC: 1712 AN: 4822

European-Finnish (FIN) AF: 0.334 AC: 3515 AN: 10534

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.269 AC: 18304 AN: 67990

Other (OTH) AF: 0.252 AC: 531 AN: 2106

Alfa AF: 0.261 Hom.: 9911

Bravo AF: 0.246

Asia WGS AF: 0.369 AC: 1284 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.27
DANN	Benign	0.55
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs12621220; hg19: chr2-113598255; COSMIC: COSV54521330;