3-144582817-C-T

Variant names:

• chr3-144582817-C-T
• rs16855659

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 0.0886 in 152,078 control chromosomes in the GnomAD database, including 743 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 0.089 (743 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0660
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.256 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: 0.0886 AC: 13460 AN: 151960 Hom.: 741 Cov.: 32

Gnomad AFR AF: 0.0730

Gnomad AMI AF: 0.0934

Gnomad AMR AF: 0.0959

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.267

Gnomad SAS AF: 0.176

Gnomad FIN AF: 0.0474

Gnomad MID AF: 0.0892

Gnomad NFE AF: 0.0805

Gnomad OTH AF: 0.0972

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

GnomAD4 genome AF: 0.0886 AC: 13476 AN: 152078 Hom.: 743 Cov.: 32 AF XY: 0.0901 AC XY: 6700 AN XY: 74324

African (AFR) AF: 0.0732 AC: 3038 AN: 41508

American (AMR) AF: 0.0957 AC: 1461 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.132 AC: 459 AN: 3472

East Asian (EAS) AF: 0.267 AC: 1379 AN: 5160

South Asian (SAS) AF: 0.177 AC: 853 AN: 4814

European-Finnish (FIN) AF: 0.0474 AC: 501 AN: 10578

Middle Eastern (MID) AF: 0.0925 AC: 27 AN: 292

European-Non Finnish (NFE) AF: 0.0804 AC: 5467 AN: 67974

Other (OTH) AF: 0.0976 AC: 206 AN: 2110

Alfa AF: 0.0798 Hom.: 700

Bravo AF: 0.0896

Asia WGS AF: 0.239 AC: 827 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.3
DANN	Benign	0.63
PhyloP100		0.066

Splicing

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

Other links and lift over

dbSNP: rs16855659; hg19: chr3-144301659;