3-142891768-A-G

Variant names:

• chr3-142891768-A-G
• rs6778966

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 0.289 in 151,952 control chromosomes in the GnomAD database, including 7,466 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 0.29 (7466 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.123
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.456 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: 0.289 AC: 43844 AN: 151836 Hom.: 7458 Cov.: 32

Gnomad AFR AF: 0.461

Gnomad AMI AF: 0.202

Gnomad AMR AF: 0.286

Gnomad ASJ AF: 0.253

Gnomad EAS AF: 0.348

Gnomad SAS AF: 0.248

Gnomad FIN AF: 0.160

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.206

Gnomad OTH AF: 0.278

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

GnomAD4 genome AF: 0.289 AC: 43881 AN: 151952 Hom.: 7466 Cov.: 32 AF XY: 0.287 AC XY: 21290 AN XY: 74292

African (AFR) AF: 0.461 AC: 19060 AN: 41302

American (AMR) AF: 0.286 AC: 4370 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.253 AC: 879 AN: 3470

East Asian (EAS) AF: 0.348 AC: 1798 AN: 5166

South Asian (SAS) AF: 0.247 AC: 1192 AN: 4828

European-Finnish (FIN) AF: 0.160 AC: 1694 AN: 10596

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.206 AC: 14024 AN: 67994

Other (OTH) AF: 0.275 AC: 580 AN: 2112

Alfa AF: 0.239 Hom.: 13465

Bravo AF: 0.307

Asia WGS AF: 0.312 AC: 1084 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.2
DANN	Benign	0.78
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs6778966; hg19: chr3-142610610;