chr21-17403962-T-C

Variant names:

• chr21-17403962-T-C
• rs7282227

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 0.0515 in 152,152 control chromosomes in the GnomAD database, including 232 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 0.052 (232 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.648

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0586 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: 0.0515 AC: 7837 AN: 152036 Hom.: 233 Cov.: 32

Gnomad AFR AF: 0.0391

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.0389

Gnomad ASJ AF: 0.0288

Gnomad EAS AF: 0.0641

Gnomad SAS AF: 0.0298

Gnomad FIN AF: 0.100

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0568

Gnomad OTH AF: 0.0455

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

GnomAD4 genome AF: 0.0515 AC: 7837 AN: 152152 Hom.: 232 Cov.: 32 AF XY: 0.0524 AC XY: 3896 AN XY: 74396

Gnomad4 AFR AF: 0.0391

Gnomad4 AMR AF: 0.0389

Gnomad4 ASJ AF: 0.0288

Gnomad4 EAS AF: 0.0642

Gnomad4 SAS AF: 0.0294

Gnomad4 FIN AF: 0.100

Gnomad4 NFE AF: 0.0568

Gnomad4 OTH AF: 0.0441

Alfa AF: 0.0542 Hom.: 319

Bravo AF: 0.0484

Asia WGS AF: 0.0410 AC: 141 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.0
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7282227; hg19: chr21-18776281;