3-166347311-T-C

Variant names:

• chr3-166347311-T-C
• rs2863381

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 152,024 control chromosomes in the GnomAD database, including 7,888 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 (7888 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.109
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.489 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	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: 43927 AN: 151908 Hom.: 7891 Cov.: 32

Gnomad AFR AF: 0.0866

Gnomad AMI AF: 0.284

Gnomad AMR AF: 0.305

Gnomad ASJ AF: 0.284

Gnomad EAS AF: 0.505

Gnomad SAS AF: 0.502

Gnomad FIN AF: 0.404

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.361

Gnomad OTH AF: 0.263

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

GnomAD4 genome AF: 0.289 AC: 43923 AN: 152024 Hom.: 7888 Cov.: 32 AF XY: 0.294 AC XY: 21879 AN XY: 74306

African (AFR) AF: 0.0863 AC: 3581 AN: 41492

American (AMR) AF: 0.304 AC: 4648 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.284 AC: 986 AN: 3470

East Asian (EAS) AF: 0.505 AC: 2606 AN: 5156

South Asian (SAS) AF: 0.504 AC: 2420 AN: 4806

European-Finnish (FIN) AF: 0.404 AC: 4260 AN: 10554

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.361 AC: 24535 AN: 67972

Other (OTH) AF: 0.265 AC: 556 AN: 2102

Alfa AF: 0.329 Hom.: 22754

Bravo AF: 0.268

Asia WGS AF: 0.482 AC: 1674 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.9
DANN	Benign	0.55
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs2863381; hg19: chr3-166065099;