rs2205445

Positions:

• chr21-28824690-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.868-2717A>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 0.0464 in 152,272 control chromosomes in the GnomAD database, including 226 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 0.046 (226 hom., cov: 32)
• Consequence: N6AMT1 XR_007067787.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.116

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 (EAS) allele frequency at 95% confidence interval = 0.148 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
N6AMT1	XR_007067787.1	n.868-2717A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0463 AC: 7052 AN: 152154 Hom.: 224 Cov.: 32

Gnomad AFR AF: 0.0578

Gnomad AMI AF: 0.0384

Gnomad AMR AF: 0.0477

Gnomad ASJ AF: 0.0963

Gnomad EAS AF: 0.156

Gnomad SAS AF: 0.0400

Gnomad FIN AF: 0.0120

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0340

Gnomad OTH AF: 0.0487

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

GnomAD4 genome AF: 0.0464 AC: 7068 AN: 152272 Hom.: 226 Cov.: 32 AF XY: 0.0463 AC XY: 3449 AN XY: 74450

Gnomad4 AFR AF: 0.0577

Gnomad4 AMR AF: 0.0485

Gnomad4 ASJ AF: 0.0963

Gnomad4 EAS AF: 0.157

Gnomad4 SAS AF: 0.0402

Gnomad4 FIN AF: 0.0120

Gnomad4 NFE AF: 0.0340

Gnomad4 OTH AF: 0.0482

Alfa AF: 0.0374 Hom.: 12

Bravo AF: 0.0515

Asia WGS AF: 0.0870 AC: 301 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	2.8
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2205445; hg19: chr21-30197012;