19-49946698-C-G

Position:

• chr19-49946698-C-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 0.597 in 151,866 control chromosomes in the GnomAD database, including 27,485 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 0.60 (27485 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14

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 (SAS) allele frequency at 95% confidence interval = 0.693 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: 0.597 AC: 90566 AN: 151748 Hom.: 27457 Cov.: 31

Gnomad AFR AF: 0.666

Gnomad AMI AF: 0.592

Gnomad AMR AF: 0.579

Gnomad ASJ AF: 0.486

Gnomad EAS AF: 0.676

Gnomad SAS AF: 0.713

Gnomad FIN AF: 0.519

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.563

Gnomad OTH AF: 0.566

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

GnomAD4 genome AF: 0.597 AC: 90647 AN: 151866 Hom.: 27485 Cov.: 31 AF XY: 0.599 AC XY: 44448 AN XY: 74216

Gnomad4 AFR AF: 0.666

Gnomad4 AMR AF: 0.579

Gnomad4 ASJ AF: 0.486

Gnomad4 EAS AF: 0.676

Gnomad4 SAS AF: 0.713

Gnomad4 FIN AF: 0.519

Gnomad4 NFE AF: 0.563

Gnomad4 OTH AF: 0.569

Alfa AF: 0.430 Hom.: 1109

Bravo AF: 0.599

Asia WGS AF: 0.714 AC: 2485 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.15
DANN	Benign	0.20

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: rs405120; hg19: chr19-50449955;