3-78565887-A-G

Position:

• chr3-78565887-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 0.857 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.857 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

Gnomad4 AFR AF: 0.729

Gnomad4 AMR AF: 0.898

Gnomad4 ASJ AF: 0.869

Gnomad4 EAS AF: 0.920

Gnomad4 SAS AF: 0.939

Gnomad4 FIN AF: 0.846

Gnomad4 NFE AF: 0.916

Gnomad4 OTH AF: 0.862

Alfa AF: 0.903 Hom.: 77129

Bravo AF: 0.852

Asia WGS AF: 0.900 AC: 3128 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.0070
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: rs6801989; hg19: chr3-78615037;