rs2054989

Variant names:

• chr3-56496681-A-G
• rs2054989

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 0.672 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
• Publications: 14 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.550 AC: 22804 AN: 41498

American (AMR) AF: 0.572 AC: 8735 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.793 AC: 2752 AN: 3472

East Asian (EAS) AF: 0.556 AC: 2875 AN: 5174

South Asian (SAS) AF: 0.768 AC: 3701 AN: 4816

European-Finnish (FIN) AF: 0.707 AC: 7481 AN: 10588

Middle Eastern (MID) AF: 0.837 AC: 246 AN: 294

European-Non Finnish (NFE) AF: 0.759 AC: 51596 AN: 67988

Other (OTH) AF: 0.683 AC: 1443 AN: 2112

Alfa AF: 0.733 Hom.: 42190

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
PhyloP100		-3.7

Splicing

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

Other links and lift over

dbSNP: rs2054989; hg19: chr3-56530709;