rs2824293

chr21-17415195-G-Achr21-17415195-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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;