chr3-80951859-A-G

Variant names:

• chr3-80951859-A-G
• rs4258921

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 0.745 in 152,092 control chromosomes in the GnomAD database, including 42,803 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 0.74 (42803 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.75

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.879 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: 0.744 AC: 113124 AN: 151974 Hom.: 42736 Cov.: 33

Gnomad AFR AF: 0.886

Gnomad AMI AF: 0.686

Gnomad AMR AF: 0.752

Gnomad ASJ AF: 0.765

Gnomad EAS AF: 0.684

Gnomad SAS AF: 0.756

Gnomad FIN AF: 0.693

Gnomad MID AF: 0.706

Gnomad NFE AF: 0.669

Gnomad OTH AF: 0.719

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

GnomAD4 genome AF: 0.745 AC: 113249 AN: 152092 Hom.: 42803 Cov.: 33 AF XY: 0.745 AC XY: 55396 AN XY: 74328

African (AFR) AF: 0.886 AC: 36798 AN: 41524

American (AMR) AF: 0.753 AC: 11486 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.765 AC: 2652 AN: 3468

East Asian (EAS) AF: 0.684 AC: 3536 AN: 5166

South Asian (SAS) AF: 0.756 AC: 3651 AN: 4828

European-Finnish (FIN) AF: 0.693 AC: 7333 AN: 10580

Middle Eastern (MID) AF: 0.718 AC: 211 AN: 294

European-Non Finnish (NFE) AF: 0.669 AC: 45440 AN: 67954

Other (OTH) AF: 0.719 AC: 1518 AN: 2112

Alfa AF: 0.713 Hom.: 4808

Bravo AF: 0.756

Asia WGS AF: 0.754 AC: 2622 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4258921; hg19: chr3-81001010;