chr21-39097594-A-G

Variant names:

• chr21-39097594-A-G
• rs378108

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.419 in 152,154 control chromosomes in the GnomAD database, including 14,660 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 0.42 (14660 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.561
• Publications: 26 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.25).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.485 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: 0.420 AC: 63800 AN: 152036 Hom.: 14664 Cov.: 33

Gnomad AFR AF: 0.241

Gnomad AMI AF: 0.374

Gnomad AMR AF: 0.443

Gnomad ASJ AF: 0.424

Gnomad EAS AF: 0.463

Gnomad SAS AF: 0.442

Gnomad FIN AF: 0.607

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.490

Gnomad OTH AF: 0.414

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

GnomAD4 genome AF: 0.419 AC: 63807 AN: 152154 Hom.: 14660 Cov.: 33 AF XY: 0.425 AC XY: 31631 AN XY: 74378

African (AFR) AF: 0.241 AC: 10026 AN: 41546

American (AMR) AF: 0.443 AC: 6768 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.424 AC: 1472 AN: 3472

East Asian (EAS) AF: 0.462 AC: 2392 AN: 5178

South Asian (SAS) AF: 0.442 AC: 2135 AN: 4828

European-Finnish (FIN) AF: 0.607 AC: 6402 AN: 10554

Middle Eastern (MID) AF: 0.405 AC: 119 AN: 294

European-Non Finnish (NFE) AF: 0.490 AC: 33284 AN: 67980

Other (OTH) AF: 0.411 AC: 868 AN: 2110

Alfa AF: 0.461 Hom.: 66634

Bravo AF: 0.398

Asia WGS AF: 0.433 AC: 1506 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.25
CADD	Benign	15
DANN	Benign	0.92
PhyloP100		0.56

Splicing

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

Other links and lift over

dbSNP: rs378108; hg19: chr21-40469520;