rs16983303

chr21-28790253-C-A

Variant summary

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

The XR_007067787.1(N6AMT1):n.936+31652G>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.207 in 152,018 control chromosomes in the GnomAD database, including 5,401 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 0.21 (5401 hom., cov: 32)
• Consequence: N6AMT1 XR_007067787.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.778

Genes affected

N6AMT1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.452 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
N6AMT1	XR_007067787.1	n.936+31652G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.207 AC: 31447 AN: 151900 Hom.: 5378 Cov.: 32

Gnomad AFR AF: 0.458

Gnomad AMI AF: 0.101

Gnomad AMR AF: 0.187

Gnomad ASJ AF: 0.186

Gnomad EAS AF: 0.368

Gnomad SAS AF: 0.130

Gnomad FIN AF: 0.0769

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.0765

Gnomad OTH AF: 0.163

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.207 AC: 31518 AN: 152018 Hom.: 5401 Cov.: 32 AF XY: 0.208 AC XY: 15424 AN XY: 74320

Gnomad4 AFR AF: 0.458

Gnomad4 AMR AF: 0.188

Gnomad4 ASJ AF: 0.186

Gnomad4 EAS AF: 0.369

Gnomad4 SAS AF: 0.130

Gnomad4 FIN AF: 0.0769

Gnomad4 NFE AF: 0.0765

Gnomad4 OTH AF: 0.164

Alfa AF: 0.132 Hom.: 604

Bravo AF: 0.228

Asia WGS AF: 0.237 AC: 821 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
Cadd	Benign	8.7
Dann	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16983303; hg19: chr21-30162575;