19-39293512-G-A

Position:

• chr19-39293512-G-A

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 0.139 in 152,006 control chromosomes in the GnomAD database, including 3,538 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 0.14 (3538 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.539

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.401 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.138 AC: 21024 AN: 151888 Hom.: 3531 Cov.: 31

Gnomad AFR AF: 0.407

Gnomad AMI AF: 0.0439

Gnomad AMR AF: 0.0624

Gnomad ASJ AF: 0.0516

Gnomad EAS AF: 0.0347

Gnomad SAS AF: 0.0504

Gnomad FIN AF: 0.0253

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0318

Gnomad OTH AF: 0.106

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

GnomAD4 genome AF: 0.139 AC: 21072 AN: 152006 Hom.: 3538 Cov.: 31 AF XY: 0.133 AC XY: 9915 AN XY: 74308

Gnomad4 AFR AF: 0.406

Gnomad4 AMR AF: 0.0621

Gnomad4 ASJ AF: 0.0516

Gnomad4 EAS AF: 0.0350

Gnomad4 SAS AF: 0.0507

Gnomad4 FIN AF: 0.0253

Gnomad4 NFE AF: 0.0318

Gnomad4 OTH AF: 0.106

Alfa AF: 0.0592 Hom.: 417

Bravo AF: 0.154

Asia WGS AF: 0.0800 AC: 278 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.98
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8107861; hg19: chr19-39784152;