rs6766000

Variant names:

• chr3-70734340-C-T
• rs6766000

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 0.204 in 152,022 control chromosomes in the GnomAD database, including 4,064 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 0.20 (4064 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.271
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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 = 0.356 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: 0.204 AC: 31002 AN: 151904 Hom.: 4043 Cov.: 32

Gnomad AFR AF: 0.361

Gnomad AMI AF: 0.112

Gnomad AMR AF: 0.242

Gnomad ASJ AF: 0.135

Gnomad EAS AF: 0.143

Gnomad SAS AF: 0.130

Gnomad FIN AF: 0.131

Gnomad MID AF: 0.169

Gnomad NFE AF: 0.127

Gnomad OTH AF: 0.188

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

GnomAD4 genome AF: 0.204 AC: 31071 AN: 152022 Hom.: 4064 Cov.: 32 AF XY: 0.202 AC XY: 15039 AN XY: 74302

African (AFR) AF: 0.361 AC: 14967 AN: 41434

American (AMR) AF: 0.242 AC: 3693 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.135 AC: 469 AN: 3468

East Asian (EAS) AF: 0.144 AC: 741 AN: 5160

South Asian (SAS) AF: 0.130 AC: 629 AN: 4822

European-Finnish (FIN) AF: 0.131 AC: 1389 AN: 10586

Middle Eastern (MID) AF: 0.171 AC: 50 AN: 292

European-Non Finnish (NFE) AF: 0.127 AC: 8639 AN: 67990

Other (OTH) AF: 0.186 AC: 392 AN: 2108

Alfa AF: 0.156 Hom.: 4281

Bravo AF: 0.224

Asia WGS AF: 0.159 AC: 559 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.1
DANN	Benign	0.40
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs6766000; hg19: chr3-70783491;