rs2832070

chr21-28765594-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+56311A>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 0.131 in 152,134 control chromosomes in the GnomAD database, including 1,455 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 0.13 (1455 hom., cov: 32)
• Consequence: N6AMT1 XR_007067787.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00400

Genes affected

N6AMT1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.18 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
N6AMT1	XR_007067787.1	n.936+56311A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.131 AC: 19854 AN: 152016 Hom.: 1446 Cov.: 32

Gnomad AFR AF: 0.183

Gnomad AMI AF: 0.0735

Gnomad AMR AF: 0.106

Gnomad ASJ AF: 0.0901

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.0823

Gnomad FIN AF: 0.0861

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.127

Gnomad OTH AF: 0.133

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

GnomAD4 genome AF: 0.131 AC: 19894 AN: 152134 Hom.: 1455 Cov.: 32 AF XY: 0.126 AC XY: 9394 AN XY: 74370

Gnomad4 AFR AF: 0.183

Gnomad4 AMR AF: 0.106

Gnomad4 ASJ AF: 0.0901

Gnomad4 EAS AF: 0.00154

Gnomad4 SAS AF: 0.0828

Gnomad4 FIN AF: 0.0861

Gnomad4 NFE AF: 0.127

Gnomad4 OTH AF: 0.131

Alfa AF: 0.123 Hom.: 657

Bravo AF: 0.132

Asia WGS AF: 0.0460 AC: 161 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	2.7
Dann	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2832070; hg19: chr21-30137916;