rs6804094

Variant names:

• chr3-187340182-A-T
• rs6804094

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 0.284 in 152,152 control chromosomes in the GnomAD database, including 7,366 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 0.28 (7366 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0800
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.437 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: 0.284 AC: 43158 AN: 152034 Hom.: 7357 Cov.: 32

Gnomad AFR AF: 0.0943

Gnomad AMI AF: 0.205

Gnomad AMR AF: 0.402

Gnomad ASJ AF: 0.235

Gnomad EAS AF: 0.453

Gnomad SAS AF: 0.292

Gnomad FIN AF: 0.352

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.352

Gnomad OTH AF: 0.291

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

GnomAD4 genome AF: 0.284 AC: 43175 AN: 152152 Hom.: 7366 Cov.: 32 AF XY: 0.286 AC XY: 21247 AN XY: 74366

African (AFR) AF: 0.0942 AC: 3913 AN: 41532

American (AMR) AF: 0.402 AC: 6148 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.235 AC: 815 AN: 3470

East Asian (EAS) AF: 0.453 AC: 2335 AN: 5158

South Asian (SAS) AF: 0.293 AC: 1414 AN: 4824

European-Finnish (FIN) AF: 0.352 AC: 3721 AN: 10574

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.352 AC: 23952 AN: 67988

Other (OTH) AF: 0.291 AC: 616 AN: 2114

Alfa AF: 0.314 Hom.: 1036

Bravo AF: 0.281

Asia WGS AF: 0.344 AC: 1196 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	3.1
DANN	Benign	0.81
PhyloP100		-0.080

Splicing

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

Other links and lift over

dbSNP: rs6804094; hg19: chr3-187057970;