rs10154126

Variant names:

• chr21-30827041-A-G
• rs10154126

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 0.43 in 152,086 control chromosomes in the GnomAD database, including 14,435 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 0.43 (14435 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0280

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.55 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: 0.430 AC: 65319 AN: 151966 Hom.: 14414 Cov.: 32

Gnomad AFR AF: 0.364

Gnomad AMI AF: 0.378

Gnomad AMR AF: 0.559

Gnomad ASJ AF: 0.384

Gnomad EAS AF: 0.446

Gnomad SAS AF: 0.502

Gnomad FIN AF: 0.460

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.432

Gnomad OTH AF: 0.446

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

GnomAD4 genome AF: 0.430 AC: 65384 AN: 152086 Hom.: 14435 Cov.: 32 AF XY: 0.432 AC XY: 32147 AN XY: 74336

Gnomad4 AFR AF: 0.364

Gnomad4 AMR AF: 0.560

Gnomad4 ASJ AF: 0.384

Gnomad4 EAS AF: 0.446

Gnomad4 SAS AF: 0.501

Gnomad4 FIN AF: 0.460

Gnomad4 NFE AF: 0.432

Gnomad4 OTH AF: 0.448

Alfa AF: 0.433 Hom.: 1827

Bravo AF: 0.434

Asia WGS AF: 0.481 AC: 1672 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.0
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10154126; hg19: chr21-32199359;