19-50744242-T-C

Position:

• chr19-50744242-T-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 0.869 in 148,944 control chromosomes in the GnomAD database, including 56,384 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 0.87 (56384 hom., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.155

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.895 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: 0.869 AC: 129382 AN: 148838 Hom.: 56333 Cov.: 22

Gnomad AFR AF: 0.823

Gnomad AMI AF: 0.834

Gnomad AMR AF: 0.893

Gnomad ASJ AF: 0.894

Gnomad EAS AF: 0.870

Gnomad SAS AF: 0.918

Gnomad FIN AF: 0.872

Gnomad MID AF: 0.870

Gnomad NFE AF: 0.887

Gnomad OTH AF: 0.866

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

GnomAD4 genome AF: 0.869 AC: 129482 AN: 148944 Hom.: 56384 Cov.: 22 AF XY: 0.869 AC XY: 62998 AN XY: 72496

Gnomad4 AFR AF: 0.823

Gnomad4 AMR AF: 0.893

Gnomad4 ASJ AF: 0.894

Gnomad4 EAS AF: 0.870

Gnomad4 SAS AF: 0.918

Gnomad4 FIN AF: 0.872

Gnomad4 NFE AF: 0.887

Gnomad4 OTH AF: 0.867

Alfa AF: 0.883 Hom.: 65789

Bravo AF: 0.867

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.4
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6509496; hg19: chr19-51247499;