rs1236427

Positions:

• chr21-28630020-A-C

Variant summary

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

The ENST00000433310.6(ENSG00000232855):​n.203-3344T>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 0.0945 in 152,162 control chromosomes in the GnomAD database, including 954 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 0.094 (954 hom., cov: 31)
• Consequence: ENST00000433310.6 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.131

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.32 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
N6AMT1	XR_007067787.1	n.937-52640T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000433310.6	n.203-3344T>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.0945 AC: 14375 AN: 152042 Hom.: 954 Cov.: 31

Gnomad AFR AF: 0.0527

Gnomad AMI AF: 0.0659

Gnomad AMR AF: 0.178

Gnomad ASJ AF: 0.0989

Gnomad EAS AF: 0.332

Gnomad SAS AF: 0.0659

Gnomad FIN AF: 0.0742

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.0877

Gnomad OTH AF: 0.114

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

GnomAD4 genome AF: 0.0945 AC: 14378 AN: 152162 Hom.: 954 Cov.: 31 AF XY: 0.0965 AC XY: 7180 AN XY: 74386

Gnomad4 AFR AF: 0.0527

Gnomad4 AMR AF: 0.178

Gnomad4 ASJ AF: 0.0989

Gnomad4 EAS AF: 0.333

Gnomad4 SAS AF: 0.0655

Gnomad4 FIN AF: 0.0742

Gnomad4 NFE AF: 0.0877

Gnomad4 OTH AF: 0.114

Alfa AF: 0.0877 Hom.: 170

Bravo AF: 0.106

Asia WGS AF: 0.192 AC: 666 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	5.1
DANN	Benign	0.92

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1236427; hg19: chr21-30002342;