14-96186284-C-T

Variant names:

• chr14-96186284-C-T
• rs874284

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 0.0688 in 152,302 control chromosomes in the GnomAD database, including 932 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 0.069 (932 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.149
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.268 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: 0.0688 AC: 10474 AN: 152184 Hom.: 933 Cov.: 32

Gnomad AFR AF: 0.0336

Gnomad AMI AF: 0.0329

Gnomad AMR AF: 0.248

Gnomad ASJ AF: 0.0190

Gnomad EAS AF: 0.280

Gnomad SAS AF: 0.0683

Gnomad FIN AF: 0.0741

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0366

Gnomad OTH AF: 0.0703

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

GnomAD4 genome AF: 0.0688 AC: 10483 AN: 152302 Hom.: 932 Cov.: 32 AF XY: 0.0755 AC XY: 5620 AN XY: 74460

African (AFR) AF: 0.0336 AC: 1395 AN: 41578

American (AMR) AF: 0.248 AC: 3794 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0190 AC: 66 AN: 3472

East Asian (EAS) AF: 0.280 AC: 1444 AN: 5164

South Asian (SAS) AF: 0.0685 AC: 331 AN: 4830

European-Finnish (FIN) AF: 0.0741 AC: 787 AN: 10620

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.0366 AC: 2488 AN: 68020

Other (OTH) AF: 0.0700 AC: 148 AN: 2114

Alfa AF: 0.0592 Hom.: 284

Bravo AF: 0.0829

Asia WGS AF: 0.165 AC: 573 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.9
DANN	Benign	0.40
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs874284; hg19: chr14-96652621;