19-7668069-C-T

Variant names:

• chr19-7668069-C-T
• rs7408174

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 0.741 in 152,194 control chromosomes in the GnomAD database, including 42,160 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 0.74 (42160 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.509
• Publications: 18 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.859 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: 0.741 AC: 112657 AN: 152076 Hom.: 42122 Cov.: 33

Gnomad AFR AF: 0.843

Gnomad AMI AF: 0.742

Gnomad AMR AF: 0.626

Gnomad ASJ AF: 0.729

Gnomad EAS AF: 0.726

Gnomad SAS AF: 0.882

Gnomad FIN AF: 0.730

Gnomad MID AF: 0.693

Gnomad NFE AF: 0.699

Gnomad OTH AF: 0.708

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

GnomAD4 genome AF: 0.741 AC: 112744 AN: 152194 Hom.: 42160 Cov.: 33 AF XY: 0.740 AC XY: 55089 AN XY: 74408

African (AFR) AF: 0.843 AC: 34989 AN: 41506

American (AMR) AF: 0.626 AC: 9574 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.729 AC: 2532 AN: 3472

East Asian (EAS) AF: 0.726 AC: 3767 AN: 5186

South Asian (SAS) AF: 0.881 AC: 4257 AN: 4832

European-Finnish (FIN) AF: 0.730 AC: 7718 AN: 10578

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

European-Non Finnish (NFE) AF: 0.699 AC: 47536 AN: 68022

Other (OTH) AF: 0.708 AC: 1491 AN: 2106

Alfa AF: 0.702 Hom.: 51706

Bravo AF: 0.734

Asia WGS AF: 0.806 AC: 2804 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.33
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs7408174; hg19: chr19-7732955;