19-39183394-A-G

Position:

• chr19-39183394-A-G

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.447

Gnomad4 AMR AF: 0.340

Gnomad4 ASJ AF: 0.517

Gnomad4 EAS AF: 0.371

Gnomad4 SAS AF: 0.335

Gnomad4 FIN AF: 0.320

Gnomad4 NFE AF: 0.389

Gnomad4 OTH AF: 0.411

Alfa AF: 0.391 Hom.: 7044

Bravo AF: 0.402

Asia WGS AF: 0.398 AC: 1384 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.54
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17641276; hg19: chr19-39674034;