3-78565887-A-G

Variant names:

• chr3-78565887-A-G
• rs6801989

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 0.857 in 152,202 control chromosomes in the GnomAD database, including 56,401 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 0.86 (56401 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.45
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.916 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.857 AC: 130362 AN: 152084 Hom.: 56382 Cov.: 33

Gnomad AFR AF: 0.730

Gnomad AMI AF: 0.840

Gnomad AMR AF: 0.897

Gnomad ASJ AF: 0.869

Gnomad EAS AF: 0.919

Gnomad SAS AF: 0.939

Gnomad FIN AF: 0.846

Gnomad MID AF: 0.899

Gnomad NFE AF: 0.916

Gnomad OTH AF: 0.864

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

GnomAD4 genome AF: 0.857 AC: 130434 AN: 152202 Hom.: 56401 Cov.: 33 AF XY: 0.856 AC XY: 63703 AN XY: 74406

African (AFR) AF: 0.729 AC: 30281 AN: 41516

American (AMR) AF: 0.898 AC: 13720 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.869 AC: 3017 AN: 3470

East Asian (EAS) AF: 0.920 AC: 4745 AN: 5160

South Asian (SAS) AF: 0.939 AC: 4535 AN: 4832

European-Finnish (FIN) AF: 0.846 AC: 8976 AN: 10612

Middle Eastern (MID) AF: 0.898 AC: 264 AN: 294

European-Non Finnish (NFE) AF: 0.916 AC: 62307 AN: 68008

Other (OTH) AF: 0.862 AC: 1825 AN: 2116

Alfa AF: 0.898 Hom.: 96871

Bravo AF: 0.852

Asia WGS AF: 0.900 AC: 3128 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.0070
DANN	Benign	0.34
PhyloP100		-2.5

Splicing

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

Other links and lift over

dbSNP: rs6801989; hg19: chr3-78615037;