rs421847

Variant names:

• chr21-18975761-G-A
• rs421847

Your query was ambiguous. Multiple possible variants found:

• chr21-18975761-G-A
• chr21-18975761-G-C

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 0.244 in 151,890 control chromosomes in the GnomAD database, including 4,611 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 0.24 (4611 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.252
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.263 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: 0.244 AC: 37098 AN: 151772 Hom.: 4600 Cov.: 31

Gnomad AFR AF: 0.217

Gnomad AMI AF: 0.258

Gnomad AMR AF: 0.258

Gnomad ASJ AF: 0.215

Gnomad EAS AF: 0.251

Gnomad SAS AF: 0.166

Gnomad FIN AF: 0.227

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.267

Gnomad OTH AF: 0.258

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

GnomAD4 genome AF: 0.244 AC: 37137 AN: 151890 Hom.: 4611 Cov.: 31 AF XY: 0.243 AC XY: 18024 AN XY: 74218

African (AFR) AF: 0.218 AC: 9017 AN: 41424

American (AMR) AF: 0.258 AC: 3929 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.215 AC: 745 AN: 3470

East Asian (EAS) AF: 0.251 AC: 1286 AN: 5130

South Asian (SAS) AF: 0.165 AC: 798 AN: 4822

European-Finnish (FIN) AF: 0.227 AC: 2388 AN: 10538

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.267 AC: 18123 AN: 67944

Other (OTH) AF: 0.259 AC: 545 AN: 2108

Alfa AF: 0.209 Hom.: 1064

Bravo AF: 0.250

Asia WGS AF: 0.213 AC: 740 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	6.5
DANN	Benign	0.88
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs421847; hg19: chr21-20348079;