rs7276141

Positions:

• chr21-28809450-G-C
• chr21-28809450-G-T

Variant summary

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

The variant allele was found at a frequency of 0.0854 in 152,142 control chromosomes in the GnomAD database, including 1,305 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 0.085 (1305 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0830

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.23 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.28809450G>C		intergenic_region
N6AMT1	XR_007067787.1	n.936+12455C>G		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0852 AC: 12959 AN: 152024 Hom.: 1301 Cov.: 32

Gnomad AFR AF: 0.234

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0938

Gnomad ASJ AF: 0.0462

Gnomad EAS AF: 0.136

Gnomad SAS AF: 0.0414

Gnomad FIN AF: 0.0298

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.00512

Gnomad OTH AF: 0.0593

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

GnomAD4 genome AF: 0.0854 AC: 12986 AN: 152142 Hom.: 1305 Cov.: 32 AF XY: 0.0867 AC XY: 6447 AN XY: 74398

Gnomad4 AFR AF: 0.233

Gnomad4 AMR AF: 0.0940

Gnomad4 ASJ AF: 0.0462

Gnomad4 EAS AF: 0.136

Gnomad4 SAS AF: 0.0408

Gnomad4 FIN AF: 0.0298

Gnomad4 NFE AF: 0.00512

Gnomad4 OTH AF: 0.0611

Alfa AF: 0.00723 Hom.: 5

Bravo AF: 0.0979

Asia WGS AF: 0.0990 AC: 343 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.24
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7276141; hg19: chr21-30181773;