rs1236428

Positions:

• chr21-28600947-C-T

Variant summary

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

The ENST00000433310.6(ENSG00000232855):​n.295-23567G>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 0.851 in 152,222 control chromosomes in the GnomAD database, including 55,599 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 0.85 (55599 hom., cov: 32)
• Consequence: ENST00000433310.6 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.176

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.93 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
N6AMT1	XR_007067787.1	n.937-23567G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000433310.6	n.295-23567G>A		intron_variant, non_coding_transcript_variant		2
	ENST00000430247.1	n.21-23567G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.851 AC: 129463 AN: 152104 Hom.: 55536 Cov.: 32

Gnomad AFR AF: 0.938

Gnomad AMI AF: 0.904

Gnomad AMR AF: 0.883

Gnomad ASJ AF: 0.927

Gnomad EAS AF: 0.915

Gnomad SAS AF: 0.837

Gnomad FIN AF: 0.778

Gnomad MID AF: 0.915

Gnomad NFE AF: 0.794

Gnomad OTH AF: 0.842

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

GnomAD4 genome AF: 0.851 AC: 129583 AN: 152222 Hom.: 55599 Cov.: 32 AF XY: 0.852 AC XY: 63445 AN XY: 74436

Gnomad4 AFR AF: 0.938

Gnomad4 AMR AF: 0.883

Gnomad4 ASJ AF: 0.927

Gnomad4 EAS AF: 0.916

Gnomad4 SAS AF: 0.837

Gnomad4 FIN AF: 0.778

Gnomad4 NFE AF: 0.794

Gnomad4 OTH AF: 0.840

Alfa AF: 0.821 Hom.: 25281

Bravo AF: 0.869

Asia WGS AF: 0.844 AC: 2937 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.7
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1236428; hg19: chr21-29973269;