rs2832010

Positions:

• chr21-28738056-T-C

Variant summary

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

The XR_007067787.1(N6AMT1):​n.936+83849A>G 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 0.228 in 151,970 control chromosomes in the GnomAD database, including 4,551 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 0.23 (4551 hom., cov: 32)
• Consequence: N6AMT1 XR_007067787.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0210

Genes affected

N6AMT1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.347 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
N6AMT1	XR_007067787.1	n.936+83849A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.228 AC: 34626 AN: 151852 Hom.: 4549 Cov.: 32

Gnomad AFR AF: 0.351

Gnomad AMI AF: 0.114

Gnomad AMR AF: 0.215

Gnomad ASJ AF: 0.257

Gnomad EAS AF: 0.253

Gnomad SAS AF: 0.279

Gnomad FIN AF: 0.224

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.151

Gnomad OTH AF: 0.220

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

GnomAD4 genome AF: 0.228 AC: 34655 AN: 151970 Hom.: 4551 Cov.: 32 AF XY: 0.232 AC XY: 17233 AN XY: 74276

Gnomad4 AFR AF: 0.351

Gnomad4 AMR AF: 0.215

Gnomad4 ASJ AF: 0.257

Gnomad4 EAS AF: 0.253

Gnomad4 SAS AF: 0.279

Gnomad4 FIN AF: 0.224

Gnomad4 NFE AF: 0.151

Gnomad4 OTH AF: 0.220

Alfa AF: 0.201 Hom.: 445

Bravo AF: 0.229

Asia WGS AF: 0.292 AC: 1018 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	7.1
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2832010; hg19: chr21-30110378;