19-40984499-G-C

Position:

• chr19-40984499-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 0.698 in 151,838 control chromosomes in the GnomAD database, including 38,476 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 0.70 (38476 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.991

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.893 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: 0.697 AC: 105812 AN: 151720 Hom.: 38426 Cov.: 29

Gnomad AFR AF: 0.900

Gnomad AMI AF: 0.440

Gnomad AMR AF: 0.758

Gnomad ASJ AF: 0.612

Gnomad EAS AF: 0.657

Gnomad SAS AF: 0.754

Gnomad FIN AF: 0.586

Gnomad MID AF: 0.725

Gnomad NFE AF: 0.585

Gnomad OTH AF: 0.686

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

GnomAD4 genome AF: 0.698 AC: 105921 AN: 151838 Hom.: 38476 Cov.: 29 AF XY: 0.700 AC XY: 51875 AN XY: 74158

Gnomad4 AFR AF: 0.901

Gnomad4 AMR AF: 0.759

Gnomad4 ASJ AF: 0.612

Gnomad4 EAS AF: 0.657

Gnomad4 SAS AF: 0.753

Gnomad4 FIN AF: 0.586

Gnomad4 NFE AF: 0.585

Gnomad4 OTH AF: 0.688

Alfa AF: 0.518 Hom.: 1537

Bravo AF: 0.717

Asia WGS AF: 0.715 AC: 2487 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	0.64
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: rs10418990; hg19: chr19-41490404;