rs464903

Positions:

• chr21-26804100-G-C
• chr21-26804100-G-T

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 0.619 in 151,956 control chromosomes in the GnomAD database, including 30,901 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 0.62 (30901 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.732 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.619 AC: 94050 AN: 151838 Hom.: 30886 Cov.: 32

Gnomad AFR AF: 0.447

Gnomad AMI AF: 0.640

Gnomad AMR AF: 0.576

Gnomad ASJ AF: 0.727

Gnomad EAS AF: 0.213

Gnomad SAS AF: 0.532

Gnomad FIN AF: 0.794

Gnomad MID AF: 0.688

Gnomad NFE AF: 0.738

Gnomad OTH AF: 0.620

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

GnomAD4 genome AF: 0.619 AC: 94101 AN: 151956 Hom.: 30901 Cov.: 32 AF XY: 0.618 AC XY: 45920 AN XY: 74264

Gnomad4 AFR AF: 0.447

Gnomad4 AMR AF: 0.575

Gnomad4 ASJ AF: 0.727

Gnomad4 EAS AF: 0.213

Gnomad4 SAS AF: 0.533

Gnomad4 FIN AF: 0.794

Gnomad4 NFE AF: 0.738

Gnomad4 OTH AF: 0.625

Alfa AF: 0.685 Hom.: 4563

Bravo AF: 0.595

Asia WGS AF: 0.403 AC: 1398 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.1
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs464903; hg19: chr21-28176419;