rs1394839

Variant names:

• chr21-25841980-A-C
• rs1394839

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 0.17 in 152,184 control chromosomes in the GnomAD database, including 2,419 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 0.17 (2419 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0500
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.228 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: 0.170 AC: 25850 AN: 152066 Hom.: 2413 Cov.: 33

Gnomad AFR AF: 0.231

Gnomad AMI AF: 0.277

Gnomad AMR AF: 0.130

Gnomad ASJ AF: 0.0911

Gnomad EAS AF: 0.00328

Gnomad SAS AF: 0.0946

Gnomad FIN AF: 0.171

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.163

Gnomad OTH AF: 0.157

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

GnomAD4 genome AF: 0.170 AC: 25891 AN: 152184 Hom.: 2419 Cov.: 33 AF XY: 0.168 AC XY: 12474 AN XY: 74410

African (AFR) AF: 0.232 AC: 9621 AN: 41518

American (AMR) AF: 0.130 AC: 1989 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0911 AC: 316 AN: 3470

East Asian (EAS) AF: 0.00348 AC: 18 AN: 5172

South Asian (SAS) AF: 0.0947 AC: 457 AN: 4826

European-Finnish (FIN) AF: 0.171 AC: 1813 AN: 10596

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.163 AC: 11059 AN: 67992

Other (OTH) AF: 0.155 AC: 329 AN: 2116

Alfa AF: 0.158 Hom.: 3043

Bravo AF: 0.169

Asia WGS AF: 0.0680 AC: 241 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.7
DANN	Benign	0.73
PhyloP100		-0.050

Splicing

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

Other links and lift over

dbSNP: rs1394839; hg19: chr21-27214291;