rs928311

Variant names:

• chr21-44985427-A-G
• rs928311

Your query was ambiguous. Multiple possible variants found:

• chr21-44985427-A-G
• chr21-44985427-A-T

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 0.557 in 152,106 control chromosomes in the GnomAD database, including 24,767 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 0.56 (24767 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.812
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.746 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.557 AC: 84712 AN: 151988 Hom.: 24759 Cov.: 34

Gnomad AFR AF: 0.375

Gnomad AMI AF: 0.562

Gnomad AMR AF: 0.565

Gnomad ASJ AF: 0.571

Gnomad EAS AF: 0.714

Gnomad SAS AF: 0.765

Gnomad FIN AF: 0.636

Gnomad MID AF: 0.640

Gnomad NFE AF: 0.626

Gnomad OTH AF: 0.590

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

GnomAD4 genome AF: 0.557 AC: 84755 AN: 152106 Hom.: 24767 Cov.: 34 AF XY: 0.561 AC XY: 41686 AN XY: 74364

African (AFR) AF: 0.374 AC: 15526 AN: 41474

American (AMR) AF: 0.565 AC: 8637 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.571 AC: 1983 AN: 3472

East Asian (EAS) AF: 0.713 AC: 3682 AN: 5162

South Asian (SAS) AF: 0.767 AC: 3693 AN: 4818

European-Finnish (FIN) AF: 0.636 AC: 6740 AN: 10592

Middle Eastern (MID) AF: 0.644 AC: 188 AN: 292

European-Non Finnish (NFE) AF: 0.626 AC: 42542 AN: 67976

Other (OTH) AF: 0.593 AC: 1253 AN: 2114

Alfa AF: 0.587 Hom.: 3355

Bravo AF: 0.538

Asia WGS AF: 0.721 AC: 2505 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	3.3
DANN	Benign	0.60
PhyloP100		-0.81

Splicing

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

Other links and lift over

dbSNP: rs928311; hg19: chr21-46405342;