rs7281691

chr21-28810789-G-Tchr21-28810789-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.936+11116C>A 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 0.111 in 152,046 control chromosomes in the GnomAD database, including 2,352 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 0.11 (2352 hom., cov: 31)
• Consequence: N6AMT1 XR_007067787.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.191

Genes affected

N6AMT1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.319 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
N6AMT1	XR_007067787.1	n.936+11116C>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.111 AC: 16888 AN: 151928 Hom.: 2345 Cov.: 31

Gnomad AFR AF: 0.324

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.103

Gnomad ASJ AF: 0.0542

Gnomad EAS AF: 0.136

Gnomad SAS AF: 0.0421

Gnomad FIN AF: 0.0296

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.00532

Gnomad OTH AF: 0.0774

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

GnomAD4 genome AF: 0.111 AC: 16921 AN: 152046 Hom.: 2352 Cov.: 31 AF XY: 0.111 AC XY: 8282 AN XY: 74340

Gnomad4 AFR AF: 0.324

Gnomad4 AMR AF: 0.103

Gnomad4 ASJ AF: 0.0542

Gnomad4 EAS AF: 0.137

Gnomad4 SAS AF: 0.0413

Gnomad4 FIN AF: 0.0296

Gnomad4 NFE AF: 0.00532

Gnomad4 OTH AF: 0.0789

Alfa AF: 0.0228 Hom.: 296

Bravo AF: 0.127

Asia WGS AF: 0.104 AC: 360 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	1.8
Dann	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7281691; hg19: chr21-30183112;