rs6773018

Variant names:

• chr3-46276560-G-A
• rs6773018

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 0.465 in 152,142 control chromosomes in the GnomAD database, including 17,508 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 0.47 (17508 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.809
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.595 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: 0.466 AC: 70769 AN: 152024 Hom.: 17493 Cov.: 32

Gnomad AFR AF: 0.602

Gnomad AMI AF: 0.432

Gnomad AMR AF: 0.361

Gnomad ASJ AF: 0.416

Gnomad EAS AF: 0.0917

Gnomad SAS AF: 0.238

Gnomad FIN AF: 0.453

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.458

Gnomad OTH AF: 0.419

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

GnomAD4 genome AF: 0.465 AC: 70813 AN: 152142 Hom.: 17508 Cov.: 32 AF XY: 0.455 AC XY: 33804 AN XY: 74376

African (AFR) AF: 0.602 AC: 24960 AN: 41480

American (AMR) AF: 0.361 AC: 5521 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.416 AC: 1443 AN: 3472

East Asian (EAS) AF: 0.0917 AC: 475 AN: 5180

South Asian (SAS) AF: 0.238 AC: 1147 AN: 4824

European-Finnish (FIN) AF: 0.453 AC: 4791 AN: 10580

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.458 AC: 31128 AN: 67982

Other (OTH) AF: 0.415 AC: 877 AN: 2114

Alfa AF: 0.466 Hom.: 2927

Bravo AF: 0.468

Asia WGS AF: 0.220 AC: 768 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.8
DANN	Benign	0.58
PhyloP100		0.81

Splicing

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

Other links and lift over

dbSNP: rs6773018; hg19: chr3-46318051;