chr21-39339551-C-A

Variant names:

• chr21-39339551-C-A
• rs2026267

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 0.304 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
• Publications: 11 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.337 AC: 13971 AN: 41450

American (AMR) AF: 0.248 AC: 3786 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.364 AC: 1262 AN: 3464

East Asian (EAS) AF: 0.0356 AC: 185 AN: 5194

South Asian (SAS) AF: 0.197 AC: 951 AN: 4826

European-Finnish (FIN) AF: 0.234 AC: 2477 AN: 10588

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.332 AC: 22601 AN: 67978

Other (OTH) AF: 0.300 AC: 634 AN: 2116

Alfa AF: 0.324 Hom.: 34663

Bravo AF: 0.308

Asia WGS AF: 0.140 AC: 488 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.25
DANN	Benign	0.82
PhyloP100		-0.62

Splicing

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

Other links and lift over

dbSNP: rs2026267; hg19: chr21-40711477;