21-39341208-G-A

Variant names:

• chr21-39341208-G-A
• rs2735306

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 151,592 control chromosomes in the GnomAD database, including 7,383 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 (7383 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0960
• Publications: 12 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.332 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.304 AC: 46098 AN: 151474 Hom.: 7381 Cov.: 31

Gnomad AFR AF: 0.337

Gnomad AMI AF: 0.362

Gnomad AMR AF: 0.248

Gnomad ASJ AF: 0.365

Gnomad EAS AF: 0.0354

Gnomad SAS AF: 0.196

Gnomad FIN AF: 0.232

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.333

Gnomad OTH AF: 0.298

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

GnomAD4 genome AF: 0.304 AC: 46107 AN: 151592 Hom.: 7383 Cov.: 31 AF XY: 0.295 AC XY: 21823 AN XY: 74028

African (AFR) AF: 0.337 AC: 13896 AN: 41270

American (AMR) AF: 0.247 AC: 3759 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.365 AC: 1264 AN: 3466

East Asian (EAS) AF: 0.0354 AC: 183 AN: 5164

South Asian (SAS) AF: 0.195 AC: 933 AN: 4794

European-Finnish (FIN) AF: 0.232 AC: 2438 AN: 10496

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

European-Non Finnish (NFE) AF: 0.333 AC: 22576 AN: 67892

Other (OTH) AF: 0.299 AC: 624 AN: 2090

Alfa AF: 0.315 Hom.: 10066

Bravo AF: 0.308

Asia WGS AF: 0.139 AC: 483 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.3
DANN	Benign	0.70
PhyloP100		0.096

Splicing

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

Other links and lift over

dbSNP: rs2735306; hg19: chr21-40713134;