rs2838970

Variant names:

• chr21-45625553-T-C
• rs2838970
• ENST00000651182.1:n.99+24A>G

Your query was ambiguous. Multiple possible variants found:

• chr21-45625553-T-C
• chr21-45625553-T-G

Variant summary

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

The ENST00000651182.1(ENSG00000286082):​n.99+24A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.566 in 151,626 control chromosomes in the GnomAD database, including 24,624 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 0.57 (24624 hom., cov: 31)
• Consequence: ENSG00000286082 ENST00000651182.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.324
• Publications: 6 publications found

Genes affected

ENSG00000286082 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.8 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286082	ENST00000651182.1	n.99+24A>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.566 AC: 85751 AN: 151508 Hom.: 24607 Cov.: 31

Gnomad AFR AF: 0.549

Gnomad AMI AF: 0.580

Gnomad AMR AF: 0.539

Gnomad ASJ AF: 0.586

Gnomad EAS AF: 0.821

Gnomad SAS AF: 0.745

Gnomad FIN AF: 0.570

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.547

Gnomad OTH AF: 0.580

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

GnomAD4 genome AF: 0.566 AC: 85808 AN: 151626 Hom.: 24624 Cov.: 31 AF XY: 0.568 AC XY: 42108 AN XY: 74096

African (AFR) AF: 0.549 AC: 22700 AN: 41314

American (AMR) AF: 0.538 AC: 8197 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.586 AC: 2032 AN: 3468

East Asian (EAS) AF: 0.821 AC: 4229 AN: 5154

South Asian (SAS) AF: 0.744 AC: 3586 AN: 4822

European-Finnish (FIN) AF: 0.570 AC: 5972 AN: 10470

Middle Eastern (MID) AF: 0.643 AC: 189 AN: 294

European-Non Finnish (NFE) AF: 0.547 AC: 37143 AN: 67864

Other (OTH) AF: 0.585 AC: 1232 AN: 2106

Alfa AF: 0.560 Hom.: 12342

Bravo AF: 0.561

Asia WGS AF: 0.787 AC: 2684 AN: 3408

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	7.3
DANN	Benign	0.79
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs2838970; hg19: chr21-47045467;