rs2830487

Variant names:

• chr21-26773870-G-A
• rs2830487

Your query was ambiguous. Multiple possible variants found:

• chr21-26773870-G-A
• chr21-26773870-G-T

Variant summary

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

The variant allele was found at a frequency of 0.403 in 151,836 control chromosomes in the GnomAD database, including 12,908 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 0.40 (12908 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.950
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.512 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

Frequencies

GnomAD3 genomes AF: 0.403 AC: 61195 AN: 151716 Hom.: 12892 Cov.: 31

Gnomad AFR AF: 0.309

Gnomad AMI AF: 0.335

Gnomad AMR AF: 0.512

Gnomad ASJ AF: 0.392

Gnomad EAS AF: 0.296

Gnomad SAS AF: 0.530

Gnomad FIN AF: 0.351

Gnomad MID AF: 0.471

Gnomad NFE AF: 0.445

Gnomad OTH AF: 0.400

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

GnomAD4 genome AF: 0.403 AC: 61226 AN: 151836 Hom.: 12908 Cov.: 31 AF XY: 0.398 AC XY: 29510 AN XY: 74202

African (AFR) AF: 0.309 AC: 12777 AN: 41400

American (AMR) AF: 0.513 AC: 7832 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.392 AC: 1361 AN: 3468

East Asian (EAS) AF: 0.295 AC: 1521 AN: 5152

South Asian (SAS) AF: 0.529 AC: 2541 AN: 4800

European-Finnish (FIN) AF: 0.351 AC: 3685 AN: 10506

Middle Eastern (MID) AF: 0.472 AC: 136 AN: 288

European-Non Finnish (NFE) AF: 0.445 AC: 30229 AN: 67942

Other (OTH) AF: 0.398 AC: 839 AN: 2110

Alfa AF: 0.430 Hom.: 17357

Bravo AF: 0.409

Asia WGS AF: 0.380 AC: 1322 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.52
DANN	Benign	0.67
PhyloP100		0.95

Splicing

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

Other links and lift over

dbSNP: rs2830487; hg19: chr21-28146189;