19-276245-T-C

Variant names:

• chr19-276245-T-C
• rs12459906

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 0.69 in 152,018 control chromosomes in the GnomAD database, including 37,649 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 0.69 (37649 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.448
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.854 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: 0.689 AC: 104727 AN: 151900 Hom.: 37599 Cov.: 31

Gnomad AFR AF: 0.861

Gnomad AMI AF: 0.684

Gnomad AMR AF: 0.716

Gnomad ASJ AF: 0.724

Gnomad EAS AF: 0.213

Gnomad SAS AF: 0.522

Gnomad FIN AF: 0.687

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.626

Gnomad OTH AF: 0.688

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

GnomAD4 genome AF: 0.690 AC: 104832 AN: 152018 Hom.: 37649 Cov.: 31 AF XY: 0.687 AC XY: 51024 AN XY: 74294

African (AFR) AF: 0.862 AC: 35738 AN: 41478

American (AMR) AF: 0.716 AC: 10937 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.724 AC: 2515 AN: 3472

East Asian (EAS) AF: 0.213 AC: 1101 AN: 5158

South Asian (SAS) AF: 0.522 AC: 2508 AN: 4806

European-Finnish (FIN) AF: 0.687 AC: 7241 AN: 10542

Middle Eastern (MID) AF: 0.690 AC: 203 AN: 294

European-Non Finnish (NFE) AF: 0.626 AC: 42521 AN: 67964

Other (OTH) AF: 0.684 AC: 1444 AN: 2112

Alfa AF: 0.649 Hom.: 47896

Bravo AF: 0.702

Asia WGS AF: 0.423 AC: 1476 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.7
DANN	Benign	0.40
PhyloP100		-0.45

Splicing

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

Other links and lift over

dbSNP: rs12459906; hg19: chr19-276245;