chr3-168119960-T-C

Variant names:

• chr3-168119960-T-C
• rs4345115

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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 0.36 (8993 hom., cov: 19)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.962
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.527 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: 0.362 AC: 47653 AN: 131788 Hom.: 8995 Cov.: 19

Gnomad AFR AF: 0.199

Gnomad AMI AF: 0.441

Gnomad AMR AF: 0.471

Gnomad ASJ AF: 0.310

Gnomad EAS AF: 0.544

Gnomad SAS AF: 0.467

Gnomad FIN AF: 0.479

Gnomad MID AF: 0.467

Gnomad NFE AF: 0.398

Gnomad OTH AF: 0.380

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

GnomAD4 genome AF: 0.361 AC: 47655 AN: 131858 Hom.: 8993 Cov.: 19 AF XY: 0.370 AC XY: 23176 AN XY: 62704

African (AFR) AF: 0.198 AC: 6807 AN: 34310

American (AMR) AF: 0.471 AC: 5548 AN: 11768

Ashkenazi Jewish (ASJ) AF: 0.310 AC: 1055 AN: 3398

East Asian (EAS) AF: 0.544 AC: 2475 AN: 4546

South Asian (SAS) AF: 0.467 AC: 1924 AN: 4122

European-Finnish (FIN) AF: 0.479 AC: 2966 AN: 6196

Middle Eastern (MID) AF: 0.447 AC: 101 AN: 226

European-Non Finnish (NFE) AF: 0.398 AC: 25728 AN: 64686

Other (OTH) AF: 0.384 AC: 664 AN: 1728

Alfa AF: 0.379 Hom.: 37193

Bravo AF: 0.337

Asia WGS AF: 0.458 AC: 1568 AN: 3430

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	7.1
DANN	Benign	0.44
PhyloP100		0.96

Splicing

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

Other links and lift over

dbSNP: rs4345115; hg19: chr3-167837748;