19-45655255-T-G

Position:

• chr19-45655255-T-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 0.349 in 151,958 control chromosomes in the GnomAD database, including 9,489 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 0.35 (9489 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.843

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.459 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: 0.349 AC: 53004 AN: 151840 Hom.: 9481 Cov.: 32

Gnomad AFR AF: 0.422

Gnomad AMI AF: 0.323

Gnomad AMR AF: 0.365

Gnomad ASJ AF: 0.384

Gnomad EAS AF: 0.474

Gnomad SAS AF: 0.335

Gnomad FIN AF: 0.299

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.299

Gnomad OTH AF: 0.350

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

GnomAD4 genome AF: 0.349 AC: 53035 AN: 151958 Hom.: 9489 Cov.: 32 AF XY: 0.350 AC XY: 25960 AN XY: 74248

Gnomad4 AFR AF: 0.422

Gnomad4 AMR AF: 0.365

Gnomad4 ASJ AF: 0.384

Gnomad4 EAS AF: 0.474

Gnomad4 SAS AF: 0.335

Gnomad4 FIN AF: 0.299

Gnomad4 NFE AF: 0.299

Gnomad4 OTH AF: 0.351

Alfa AF: 0.310 Hom.: 13447

Bravo AF: 0.358

Asia WGS AF: 0.396 AC: 1379 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	2.3
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8108269; hg19: chr19-46158513;