19-276245-T-C

Position:

• chr19-276245-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 0.69 in 152,018 control chromosomes in the GnomAD database, including 37,649 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 0.69 (37649 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.448

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 = 0.854 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: 0.689 AC: 104727 AN: 151900 Hom.: 37599 Cov.: 31

Gnomad AFR AF: 0.861

Gnomad AMI AF: 0.684

Gnomad AMR AF: 0.716

Gnomad ASJ AF: 0.724

Gnomad EAS AF: 0.213

Gnomad SAS AF: 0.522

Gnomad FIN AF: 0.687

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.626

Gnomad OTH AF: 0.688

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

GnomAD4 genome AF: 0.690 AC: 104832 AN: 152018 Hom.: 37649 Cov.: 31 AF XY: 0.687 AC XY: 51024 AN XY: 74294

Gnomad4 AFR AF: 0.862

Gnomad4 AMR AF: 0.716

Gnomad4 ASJ AF: 0.724

Gnomad4 EAS AF: 0.213

Gnomad4 SAS AF: 0.522

Gnomad4 FIN AF: 0.687

Gnomad4 NFE AF: 0.626

Gnomad4 OTH AF: 0.684

Alfa AF: 0.639 Hom.: 36323

Bravo AF: 0.702

Asia WGS AF: 0.423 AC: 1476 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	1.7
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12459906; hg19: chr19-276245;