rs7282227

Variant names:

• chr21-17403962-T-C
• rs7282227

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 0.0515 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.0391 AC: 1623 AN: 41520

American (AMR) AF: 0.0389 AC: 594 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0288 AC: 100 AN: 3468

East Asian (EAS) AF: 0.0642 AC: 332 AN: 5168

South Asian (SAS) AF: 0.0294 AC: 142 AN: 4824

European-Finnish (FIN) AF: 0.100 AC: 1064 AN: 10592

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0568 AC: 3860 AN: 67992

Other (OTH) AF: 0.0441 AC: 93 AN: 2110

Alfa AF: 0.0537 Hom.: 407

Bravo AF: 0.0484

Asia WGS AF: 0.0410 AC: 141 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.0
DANN	Benign	0.64
PhyloP100		0.65

Splicing

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

Other links and lift over

dbSNP: rs7282227; hg19: chr21-18776281;