rs2026267

Variant names:

• chr21-39339551-C-A
• rs2026267

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 0.304 in 152,106 control chromosomes in the GnomAD database, including 7,409 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 0.30 (7409 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.618

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.332 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: 0.305 AC: 46286 AN: 151988 Hom.: 7406 Cov.: 33

Gnomad AFR AF: 0.337

Gnomad AMI AF: 0.362

Gnomad AMR AF: 0.248

Gnomad ASJ AF: 0.364

Gnomad EAS AF: 0.0355

Gnomad SAS AF: 0.198

Gnomad FIN AF: 0.234

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.332

Gnomad OTH AF: 0.299

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

GnomAD4 genome AF: 0.304 AC: 46301 AN: 152106 Hom.: 7409 Cov.: 33 AF XY: 0.295 AC XY: 21964 AN XY: 74388

Gnomad4 AFR AF: 0.337

Gnomad4 AMR AF: 0.248

Gnomad4 ASJ AF: 0.364

Gnomad4 EAS AF: 0.0356

Gnomad4 SAS AF: 0.197

Gnomad4 FIN AF: 0.234

Gnomad4 NFE AF: 0.332

Gnomad4 OTH AF: 0.300

Alfa AF: 0.330 Hom.: 16783

Bravo AF: 0.308

Asia WGS AF: 0.140 AC: 488 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.25
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2026267; hg19: chr21-40711477;