rs2824293

Variant names:

• chr21-17415195-G-A
• rs2824293

Your query was ambiguous. Multiple possible variants found:

• chr21-17415195-G-A
• chr21-17415195-G-C

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 0.538 in 151,824 control chromosomes in the GnomAD database, including 22,067 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 0.54 (22067 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.741
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.574 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: 0.538 AC: 81558 AN: 151704 Hom.: 22051 Cov.: 31

Gnomad AFR AF: 0.525

Gnomad AMI AF: 0.540

Gnomad AMR AF: 0.534

Gnomad ASJ AF: 0.566

Gnomad EAS AF: 0.452

Gnomad SAS AF: 0.593

Gnomad FIN AF: 0.561

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.544

Gnomad OTH AF: 0.524

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

GnomAD4 genome AF: 0.538 AC: 81632 AN: 151824 Hom.: 22067 Cov.: 31 AF XY: 0.541 AC XY: 40120 AN XY: 74182

African (AFR) AF: 0.526 AC: 21746 AN: 41380

American (AMR) AF: 0.534 AC: 8144 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.566 AC: 1962 AN: 3464

East Asian (EAS) AF: 0.452 AC: 2319 AN: 5130

South Asian (SAS) AF: 0.592 AC: 2850 AN: 4812

European-Finnish (FIN) AF: 0.561 AC: 5904 AN: 10532

Middle Eastern (MID) AF: 0.507 AC: 149 AN: 294

European-Non Finnish (NFE) AF: 0.544 AC: 36955 AN: 67948

Other (OTH) AF: 0.528 AC: 1112 AN: 2106

Alfa AF: 0.535 Hom.: 28955

Bravo AF: 0.532

Asia WGS AF: 0.565 AC: 1964 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.3
DANN	Benign	0.71
PhyloP100		-0.74

Splicing

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

Other links and lift over

dbSNP: rs2824293; hg19: chr21-18787514;