rs10854467

Variant names:

• chr21-44987735-C-G
• rs10854467

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 0.406 in 152,128 control chromosomes in the GnomAD database, including 14,473 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 0.41 (14473 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0430
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.631 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: 0.406 AC: 61713 AN: 152010 Hom.: 14472 Cov.: 34

Gnomad AFR AF: 0.163

Gnomad AMI AF: 0.474

Gnomad AMR AF: 0.450

Gnomad ASJ AF: 0.404

Gnomad EAS AF: 0.641

Gnomad SAS AF: 0.649

Gnomad FIN AF: 0.538

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.487

Gnomad OTH AF: 0.429

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

GnomAD4 genome AF: 0.406 AC: 61729 AN: 152128 Hom.: 14473 Cov.: 34 AF XY: 0.414 AC XY: 30819 AN XY: 74372

African (AFR) AF: 0.162 AC: 6745 AN: 41546

American (AMR) AF: 0.451 AC: 6888 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.404 AC: 1402 AN: 3470

East Asian (EAS) AF: 0.641 AC: 3305 AN: 5160

South Asian (SAS) AF: 0.650 AC: 3135 AN: 4826

European-Finnish (FIN) AF: 0.538 AC: 5698 AN: 10586

Middle Eastern (MID) AF: 0.408 AC: 120 AN: 294

European-Non Finnish (NFE) AF: 0.487 AC: 33098 AN: 67944

Other (OTH) AF: 0.430 AC: 907 AN: 2108

Alfa AF: 0.442 Hom.: 2027

Bravo AF: 0.384

Asia WGS AF: 0.598 AC: 2079 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	1.4
DANN	Benign	0.69
PhyloP100		-0.043

Splicing

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

Other links and lift over

dbSNP: rs10854467; hg19: chr21-46407650; COSMIC: COSV71375279;