19-39183394-A-G

Variant names:

• chr19-39183394-A-G
• rs17641276

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 0.396 in 152,100 control chromosomes in the GnomAD database, including 12,093 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 0.40 (12093 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.441 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.396 AC: 60174 AN: 151982 Hom.: 12079 Cov.: 32

Gnomad AFR AF: 0.446

Gnomad AMI AF: 0.409

Gnomad AMR AF: 0.340

Gnomad ASJ AF: 0.517

Gnomad EAS AF: 0.371

Gnomad SAS AF: 0.336

Gnomad FIN AF: 0.320

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.389

Gnomad OTH AF: 0.411

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

GnomAD4 genome AF: 0.396 AC: 60245 AN: 152100 Hom.: 12093 Cov.: 32 AF XY: 0.390 AC XY: 28966 AN XY: 74356

African (AFR) AF: 0.447 AC: 18528 AN: 41484

American (AMR) AF: 0.340 AC: 5192 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.517 AC: 1794 AN: 3468

East Asian (EAS) AF: 0.371 AC: 1917 AN: 5174

South Asian (SAS) AF: 0.335 AC: 1615 AN: 4820

European-Finnish (FIN) AF: 0.320 AC: 3387 AN: 10590

Middle Eastern (MID) AF: 0.435 AC: 128 AN: 294

European-Non Finnish (NFE) AF: 0.389 AC: 26445 AN: 67980

Other (OTH) AF: 0.411 AC: 867 AN: 2108

Alfa AF: 0.392 Hom.: 12188

Bravo AF: 0.402

Asia WGS AF: 0.398 AC: 1384 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	0.54
DANN	Benign	0.44
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs17641276; hg19: chr19-39674034;