rs2826629

chr21-20971699-T-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 0.346 in 151,946 control chromosomes in the GnomAD database, including 9,329 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 0.35 (9329 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.139

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.364 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: 0.346 AC: 52479 AN: 151828 Hom.: 9324 Cov.: 32

Gnomad AFR AF: 0.336

Gnomad AMI AF: 0.268

Gnomad AMR AF: 0.321

Gnomad ASJ AF: 0.368

Gnomad EAS AF: 0.144

Gnomad SAS AF: 0.375

Gnomad FIN AF: 0.357

Gnomad MID AF: 0.417

Gnomad NFE AF: 0.368

Gnomad OTH AF: 0.353

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

GnomAD4 genome AF: 0.346 AC: 52518 AN: 151946 Hom.: 9329 Cov.: 32 AF XY: 0.345 AC XY: 25617 AN XY: 74266

Gnomad4 AFR AF: 0.336

Gnomad4 AMR AF: 0.321

Gnomad4 ASJ AF: 0.368

Gnomad4 EAS AF: 0.145

Gnomad4 SAS AF: 0.376

Gnomad4 FIN AF: 0.357

Gnomad4 NFE AF: 0.368

Gnomad4 OTH AF: 0.354

Alfa AF: 0.361 Hom.: 4460

Bravo AF: 0.340

Asia WGS AF: 0.285 AC: 989 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	2.0
Dann	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2826629; hg19: chr21-22344016;