chr19-39252463-A-T

Position:

• chr19-39252463-A-T

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 0.285 in 152,166 control chromosomes in the GnomAD database, including 6,454 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 0.28 (6454 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.14

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.334 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: 0.285 AC: 43296 AN: 152048 Hom.: 6448 Cov.: 32

Gnomad AFR AF: 0.297

Gnomad AMI AF: 0.336

Gnomad AMR AF: 0.342

Gnomad ASJ AF: 0.389

Gnomad EAS AF: 0.0711

Gnomad SAS AF: 0.209

Gnomad FIN AF: 0.212

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.291

Gnomad OTH AF: 0.297

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

GnomAD4 genome AF: 0.285 AC: 43343 AN: 152166 Hom.: 6454 Cov.: 32 AF XY: 0.279 AC XY: 20731 AN XY: 74404

Gnomad4 AFR AF: 0.298

Gnomad4 AMR AF: 0.341

Gnomad4 ASJ AF: 0.389

Gnomad4 EAS AF: 0.0715

Gnomad4 SAS AF: 0.210

Gnomad4 FIN AF: 0.212

Gnomad4 NFE AF: 0.291

Gnomad4 OTH AF: 0.294

Alfa AF: 0.298 Hom.: 841

Bravo AF: 0.298

Asia WGS AF: 0.149 AC: 520 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	10
DANN	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8113007; hg19: chr19-39743103;