3-42228578-G-C

Variant names:

• chr3-42228578-G-C
• rs6809785

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 0.175 in 152,132 control chromosomes in the GnomAD database, including 4,597 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 0.18 (4597 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.470
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.443 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.175 AC: 26606 AN: 152014 Hom.: 4578 Cov.: 32

Gnomad AFR AF: 0.448

Gnomad AMI AF: 0.00658

Gnomad AMR AF: 0.0943

Gnomad ASJ AF: 0.0738

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0626

Gnomad FIN AF: 0.0645

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0745

Gnomad OTH AF: 0.147

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

GnomAD4 genome AF: 0.175 AC: 26663 AN: 152132 Hom.: 4597 Cov.: 32 AF XY: 0.170 AC XY: 12623 AN XY: 74392

African (AFR) AF: 0.448 AC: 18572 AN: 41436

American (AMR) AF: 0.0942 AC: 1440 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0738 AC: 256 AN: 3468

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5186

South Asian (SAS) AF: 0.0629 AC: 303 AN: 4820

European-Finnish (FIN) AF: 0.0645 AC: 684 AN: 10606

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.0744 AC: 5062 AN: 68008

Other (OTH) AF: 0.145 AC: 306 AN: 2108

Alfa AF: 0.142 Hom.: 373

Bravo AF: 0.190

Asia WGS AF: 0.0640 AC: 224 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.4
DANN	Benign	0.53
PhyloP100		0.47

Splicing

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

Other links and lift over

dbSNP: rs6809785; hg19: chr3-42270070;