chr21-25457465-C-T

Variant names:

• chr21-25457465-C-T
• rs12483240
• ENST00000779085.1:n.616-4039G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_188560.1(LOC105372753):​n.884-4039G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0752 in 152,164 control chromosomes in the GnomAD database, including 842 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 0.075 (842 hom., cov: 32)
• Consequence: LOC105372753 NR_188560.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0910
• Publications: 6 publications found

Genes affected

ENSG00000229962 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.229 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_188560.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC105372753	NR_188560.1		n.884-4039G>A		intron	N/A
	LOC105372753	NR_188564.1		n.491-4039G>A		intron	N/A
	LOC105372753	NR_188566.1		n.373-4039G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000229962	ENST00000779085.1		n.616-4039G>A		intron	N/A
	ENSG00000229962	ENST00000779086.1		n.658-4039G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0749 AC: 11394 AN: 152046 Hom.: 827 Cov.: 32

Gnomad AFR AF: 0.0671

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.235

Gnomad ASJ AF: 0.0251

Gnomad EAS AF: 0.130

Gnomad SAS AF: 0.105

Gnomad FIN AF: 0.0657

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0430

Gnomad OTH AF: 0.0672

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

GnomAD4 genome AF: 0.0752 AC: 11440 AN: 152164 Hom.: 842 Cov.: 32 AF XY: 0.0798 AC XY: 5939 AN XY: 74394

African (AFR) AF: 0.0674 AC: 2801 AN: 41528

American (AMR) AF: 0.236 AC: 3600 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0251 AC: 87 AN: 3470

East Asian (EAS) AF: 0.130 AC: 674 AN: 5178

South Asian (SAS) AF: 0.105 AC: 504 AN: 4808

European-Finnish (FIN) AF: 0.0657 AC: 696 AN: 10592

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0430 AC: 2925 AN: 68008

Other (OTH) AF: 0.0693 AC: 146 AN: 2106

Alfa AF: 0.0520 Hom.: 409

Bravo AF: 0.0909

Asia WGS AF: 0.158 AC: 547 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	7.8
DANN	Benign	0.48
PhyloP100		-0.091

Splicing

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

Other links and lift over

dbSNP: rs12483240; hg19: chr21-26829777;