rs6780569

Variant names:

• chr3-23156993-G-A
• rs6780569

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 0.242 in 151,636 control chromosomes in the GnomAD database, including 7,371 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 0.24 (7371 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.729
• Publications: 36 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.544 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: 0.242 AC: 36663 AN: 151518 Hom.: 7345 Cov.: 32

Gnomad AFR AF: 0.549

Gnomad AMI AF: 0.183

Gnomad AMR AF: 0.134

Gnomad ASJ AF: 0.0912

Gnomad EAS AF: 0.184

Gnomad SAS AF: 0.279

Gnomad FIN AF: 0.173

Gnomad MID AF: 0.169

Gnomad NFE AF: 0.102

Gnomad OTH AF: 0.213

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

GnomAD4 genome AF: 0.242 AC: 36734 AN: 151636 Hom.: 7371 Cov.: 32 AF XY: 0.244 AC XY: 18090 AN XY: 74108

African (AFR) AF: 0.550 AC: 22727 AN: 41334

American (AMR) AF: 0.133 AC: 2034 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.0912 AC: 316 AN: 3466

East Asian (EAS) AF: 0.184 AC: 950 AN: 5156

South Asian (SAS) AF: 0.277 AC: 1332 AN: 4802

European-Finnish (FIN) AF: 0.173 AC: 1821 AN: 10500

Middle Eastern (MID) AF: 0.161 AC: 47 AN: 292

European-Non Finnish (NFE) AF: 0.102 AC: 6891 AN: 67820

Other (OTH) AF: 0.213 AC: 449 AN: 2106

Alfa AF: 0.150 Hom.: 9293

Bravo AF: 0.250

Asia WGS AF: 0.274 AC: 953 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.56
DANN	Benign	0.63
PhyloP100		-0.73

Splicing

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

Other links and lift over

dbSNP: rs6780569; hg19: chr3-23198484;