rs1394839

Positions:

• chr21-25841980-A-C

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 0.17 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.232

Gnomad4 AMR AF: 0.130

Gnomad4 ASJ AF: 0.0911

Gnomad4 EAS AF: 0.00348

Gnomad4 SAS AF: 0.0947

Gnomad4 FIN AF: 0.171

Gnomad4 NFE AF: 0.163

Gnomad4 OTH AF: 0.155

Alfa AF: 0.156 Hom.: 2022

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1394839; hg19: chr21-27214291;