rs9985076

chr21-28858882-G-A

Variant summary

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

The XR_007067787.1(N6AMT1):n.867+13731C>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 0.0783 in 151,986 control chromosomes in the GnomAD database, including 1,112 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 0.078 (1112 hom., cov: 32)
• Consequence: N6AMT1 XR_007067787.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.440

Genes affected

N6AMT1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.209 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
N6AMT1	XR_007067787.1	n.867+13731C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0782 AC: 11874 AN: 151868 Hom.: 1113 Cov.: 32

Gnomad AFR AF: 0.213

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0934

Gnomad ASJ AF: 0.0452

Gnomad EAS AF: 0.145

Gnomad SAS AF: 0.0721

Gnomad FIN AF: 0.00142

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.00412

Gnomad OTH AF: 0.0541

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

GnomAD4 genome AF: 0.0783 AC: 11894 AN: 151986 Hom.: 1112 Cov.: 32 AF XY: 0.0784 AC XY: 5823 AN XY: 74306

Gnomad4 AFR AF: 0.212

Gnomad4 AMR AF: 0.0934

Gnomad4 ASJ AF: 0.0452

Gnomad4 EAS AF: 0.145

Gnomad4 SAS AF: 0.0717

Gnomad4 FIN AF: 0.00142

Gnomad4 NFE AF: 0.00412

Gnomad4 OTH AF: 0.0559

Alfa AF: 0.0487 Hom.: 94

Bravo AF: 0.0918

Asia WGS AF: 0.112 AC: 389 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	2.7
Dann	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9985076; hg19: chr21-30231204;