19-40859445-A-T

Position:

• chr19-40859445-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 0.0443 in 150,982 control chromosomes in the GnomAD database, including 405 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 0.044 (405 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0627 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: 0.0443 AC: 6686 AN: 150866 Hom.: 404 Cov.: 31

Gnomad AFR AF: 0.0112

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0175

Gnomad ASJ AF: 0.0573

Gnomad EAS AF: 0.0326

Gnomad SAS AF: 0.0442

Gnomad FIN AF: 0.0906

Gnomad MID AF: 0.0478

Gnomad NFE AF: 0.0643

Gnomad OTH AF: 0.0371

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

GnomAD4 genome AF: 0.0443 AC: 6688 AN: 150982 Hom.: 405 Cov.: 31 AF XY: 0.0446 AC XY: 3282 AN XY: 73664

Gnomad4 AFR AF: 0.0112

Gnomad4 AMR AF: 0.0174

Gnomad4 ASJ AF: 0.0573

Gnomad4 EAS AF: 0.0327

Gnomad4 SAS AF: 0.0448

Gnomad4 FIN AF: 0.0906

Gnomad4 NFE AF: 0.0643

Gnomad4 OTH AF: 0.0368

Alfa AF: 0.0556 Hom.: 56

Bravo AF: 0.0379

Asia WGS AF: 0.0410 AC: 140 AN: 3428

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.7
DANN	Benign	0.35

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs7255616; hg19: chr19-41365350;