rs2054989

Positions:

• chr3-56496681-A-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 0.672 in 152,130 control chromosomes in the GnomAD database, including 35,242 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 0.67 (35242 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.74

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.753 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: 0.672 AC: 102190 AN: 152012 Hom.: 35232 Cov.: 33

Gnomad AFR AF: 0.549

Gnomad AMI AF: 0.679

Gnomad AMR AF: 0.573

Gnomad ASJ AF: 0.793

Gnomad EAS AF: 0.556

Gnomad SAS AF: 0.768

Gnomad FIN AF: 0.707

Gnomad MID AF: 0.848

Gnomad NFE AF: 0.759

Gnomad OTH AF: 0.684

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

GnomAD4 genome AF: 0.672 AC: 102252 AN: 152130 Hom.: 35242 Cov.: 33 AF XY: 0.669 AC XY: 49738 AN XY: 74368

Gnomad4 AFR AF: 0.550

Gnomad4 AMR AF: 0.572

Gnomad4 ASJ AF: 0.793

Gnomad4 EAS AF: 0.556

Gnomad4 SAS AF: 0.768

Gnomad4 FIN AF: 0.707

Gnomad4 NFE AF: 0.759

Gnomad4 OTH AF: 0.683

Alfa AF: 0.737 Hom.: 17610

Bravo AF: 0.655

Asia WGS AF: 0.663 AC: 2304 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.17
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2054989; hg19: chr3-56530709;