rs10854467

Positions:

• chr21-44987735-C-G

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 0.406 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.162

Gnomad4 AMR AF: 0.451

Gnomad4 ASJ AF: 0.404

Gnomad4 EAS AF: 0.641

Gnomad4 SAS AF: 0.650

Gnomad4 FIN AF: 0.538

Gnomad4 NFE AF: 0.487

Gnomad4 OTH AF: 0.430

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

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