rs8108392

Positions:

• chr19-39293432-T-C

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 0.151 in 152,018 control chromosomes in the GnomAD database, including 4,271 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 0.15 (4271 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0330

ACMG classification

Verdict is Benign. Variant got -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 = 0.441 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: 0.150 AC: 22842 AN: 151900 Hom.: 4260 Cov.: 31

Gnomad AFR AF: 0.447

Gnomad AMI AF: 0.0439

Gnomad AMR AF: 0.0663

Gnomad ASJ AF: 0.0723

Gnomad EAS AF: 0.0347

Gnomad SAS AF: 0.0516

Gnomad FIN AF: 0.0253

Gnomad MID AF: 0.0446

Gnomad NFE AF: 0.0320

Gnomad OTH AF: 0.116

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

GnomAD4 genome AF: 0.151 AC: 22895 AN: 152018 Hom.: 4271 Cov.: 31 AF XY: 0.145 AC XY: 10781 AN XY: 74336

Gnomad4 AFR AF: 0.446

Gnomad4 AMR AF: 0.0661

Gnomad4 ASJ AF: 0.0723

Gnomad4 EAS AF: 0.0347

Gnomad4 SAS AF: 0.0517

Gnomad4 FIN AF: 0.0253

Gnomad4 NFE AF: 0.0320

Gnomad4 OTH AF: 0.116

Alfa AF: 0.0526 Hom.: 559

Bravo AF: 0.168

Asia WGS AF: 0.0820 AC: 285 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	5.2
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8108392; hg19: chr19-39784072;