chr21-19620852-G-A

Position:

• chr21-19620852-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000603349.1(NIPA2P3):​n.158G>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 0.0618 in 152,192 control chromosomes in the GnomAD database, including 822 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 0.062 (822 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: NIPA2P3 ENST00000603349.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.20

Genes affected

NIPA2P3 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.184 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NIPA2P3		n.19620852G>A		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NIPA2P3	ENST00000603349.1	n.158G>A		non_coding_transcript_exon_variant	1/1	6

Frequencies

GnomAD3 genomes AF: 0.0615 AC: 9352 AN: 152074 Hom.: 811 Cov.: 32

Gnomad AFR AF: 0.187

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0296

Gnomad ASJ AF: 0.0294

Gnomad EAS AF: 0.139

Gnomad SAS AF: 0.0151

Gnomad FIN AF: 0.00104

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.00231

Gnomad OTH AF: 0.0449

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 6 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 4

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome AF: 0.0618 AC: 9401 AN: 152192 Hom.: 822 Cov.: 32 AF XY: 0.0609 AC XY: 4528 AN XY: 74404

Gnomad4 AFR AF: 0.188

Gnomad4 AMR AF: 0.0295

Gnomad4 ASJ AF: 0.0294

Gnomad4 EAS AF: 0.139

Gnomad4 SAS AF: 0.0149

Gnomad4 FIN AF: 0.00104

Gnomad4 NFE AF: 0.00231

Gnomad4 OTH AF: 0.0454

Alfa AF: 0.0400 Hom.: 66

Bravo AF: 0.0711

Asia WGS AF: 0.0810 AC: 281 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.6
DANN	Benign	0.17

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9305918; hg19: chr21-20993166;