rs6789987

Variant names:

• chr3-188045610-C-T
• rs6789987

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 0.306 in 151,872 control chromosomes in the GnomAD database, including 7,786 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 0.31 (7786 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.251

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.443 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: 0.306 AC: 46408 AN: 151752 Hom.: 7770 Cov.: 31

Gnomad AFR AF: 0.449

Gnomad AMI AF: 0.285

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.286

Gnomad EAS AF: 0.136

Gnomad SAS AF: 0.146

Gnomad FIN AF: 0.319

Gnomad MID AF: 0.140

Gnomad NFE AF: 0.269

Gnomad OTH AF: 0.284

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

GnomAD4 genome AF: 0.306 AC: 46459 AN: 151872 Hom.: 7786 Cov.: 31 AF XY: 0.301 AC XY: 22365 AN XY: 74234

Gnomad4 AFR AF: 0.449

Gnomad4 AMR AF: 0.195

Gnomad4 ASJ AF: 0.286

Gnomad4 EAS AF: 0.136

Gnomad4 SAS AF: 0.146

Gnomad4 FIN AF: 0.319

Gnomad4 NFE AF: 0.269

Gnomad4 OTH AF: 0.281

Alfa AF: 0.265 Hom.: 5570

Bravo AF: 0.306

Asia WGS AF: 0.141 AC: 490 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.33
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6789987; hg19: chr3-187763398;