rs8130766

chr21-28778098-G-Tchr21-28778098-G-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+43807C>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 0.0815 in 152,150 control chromosomes in the GnomAD database, including 1,163 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 0.081 (1163 hom., cov: 32)
• Consequence: N6AMT1 XR_007067787.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0820

Genes affected

N6AMT1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.08).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.213 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
N6AMT1	XR_007067787.1	n.936+43807C>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0814 AC: 12370 AN: 152032 Hom.: 1162 Cov.: 32

Gnomad AFR AF: 0.217

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0929

Gnomad ASJ AF: 0.0461

Gnomad EAS AF: 0.146

Gnomad SAS AF: 0.0398

Gnomad FIN AF: 0.0364

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.00532

Gnomad OTH AF: 0.0589

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

GnomAD4 genome AF: 0.0815 AC: 12393 AN: 152150 Hom.: 1163 Cov.: 32 AF XY: 0.0828 AC XY: 6158 AN XY: 74378

Gnomad4 AFR AF: 0.216

Gnomad4 AMR AF: 0.0931

Gnomad4 ASJ AF: 0.0461

Gnomad4 EAS AF: 0.146

Gnomad4 SAS AF: 0.0396

Gnomad4 FIN AF: 0.0364

Gnomad4 NFE AF: 0.00532

Gnomad4 OTH AF: 0.0601

Alfa AF: 0.0255 Hom.: 35

Bravo AF: 0.0928

Asia WGS AF: 0.0990 AC: 345 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
Cadd	Benign	0.47
Dann	Benign	0.17

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8130766; hg19: chr21-30150420;