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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.526

Gnomad4 AMR AF: 0.534

Gnomad4 ASJ AF: 0.566

Gnomad4 EAS AF: 0.452

Gnomad4 SAS AF: 0.592

Gnomad4 FIN AF: 0.561

Gnomad4 NFE AF: 0.544

Gnomad4 OTH AF: 0.528

Alfa AF: 0.530 Hom.: 3069

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2824293; hg19: chr21-18787514;