rs2839520

Variant names:

• chr21-42449553-G-A
• rs2839520
• ENST00000824420.1:n.507C>T

Variant summary

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

The ENST00000824420.1(ENSG00000307177):​n.507C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.466 in 151,786 control chromosomes in the GnomAD database, including 17,200 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 0.47 (17200 hom., cov: 31)
• Consequence: ENSG00000307177 ENST00000824420.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.70
• Publications: 8 publications found

Genes affected

ENSG00000307177 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.533 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
ENSG00000307177	ENST00000824420.1	n.507C>T		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000307177	ENST00000824421.1	n.332C>T		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.466 AC: 70700 AN: 151668 Hom.: 17200 Cov.: 31

Gnomad AFR AF: 0.333

Gnomad AMI AF: 0.363

Gnomad AMR AF: 0.413

Gnomad ASJ AF: 0.362

Gnomad EAS AF: 0.484

Gnomad SAS AF: 0.526

Gnomad FIN AF: 0.610

Gnomad MID AF: 0.341

Gnomad NFE AF: 0.538

Gnomad OTH AF: 0.491

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

GnomAD4 genome AF: 0.466 AC: 70718 AN: 151786 Hom.: 17200 Cov.: 31 AF XY: 0.468 AC XY: 34734 AN XY: 74160

African (AFR) AF: 0.333 AC: 13771 AN: 41388

American (AMR) AF: 0.412 AC: 6289 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.362 AC: 1254 AN: 3468

East Asian (EAS) AF: 0.484 AC: 2497 AN: 5156

South Asian (SAS) AF: 0.527 AC: 2535 AN: 4810

European-Finnish (FIN) AF: 0.610 AC: 6423 AN: 10526

Middle Eastern (MID) AF: 0.325 AC: 95 AN: 292

European-Non Finnish (NFE) AF: 0.538 AC: 36500 AN: 67886

Other (OTH) AF: 0.487 AC: 1024 AN: 2102

Alfa AF: 0.502 Hom.: 62301

Bravo AF: 0.446

Asia WGS AF: 0.490 AC: 1708 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.12
DANN	Benign	0.58
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs2839520; hg19: chr21-43869663;