19-33367307-G-C

Position:

• chr19-33367307-G-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 0.528 in 151,932 control chromosomes in the GnomAD database, including 21,414 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 0.53 (21414 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.995

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 = 0.581 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: 0.528 AC: 80155 AN: 151814 Hom.: 21394 Cov.: 31

Gnomad AFR AF: 0.587

Gnomad AMI AF: 0.451

Gnomad AMR AF: 0.518

Gnomad ASJ AF: 0.493

Gnomad EAS AF: 0.396

Gnomad SAS AF: 0.372

Gnomad FIN AF: 0.534

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.517

Gnomad OTH AF: 0.539

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

GnomAD4 genome AF: 0.528 AC: 80216 AN: 151932 Hom.: 21414 Cov.: 31 AF XY: 0.526 AC XY: 39031 AN XY: 74266

Gnomad4 AFR AF: 0.587

Gnomad4 AMR AF: 0.519

Gnomad4 ASJ AF: 0.493

Gnomad4 EAS AF: 0.396

Gnomad4 SAS AF: 0.373

Gnomad4 FIN AF: 0.534

Gnomad4 NFE AF: 0.517

Gnomad4 OTH AF: 0.534

Alfa AF: 0.367 Hom.: 913

Bravo AF: 0.534

Asia WGS AF: 0.371 AC: 1292 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	0.47
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs736682; hg19: chr19-33858213;