19-55372511-C-T

Variant names:

• chr19-55372511-C-T
• rs6509940

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 0.527 in 151,896 control chromosomes in the GnomAD database, including 21,234 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 0.53 (21234 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.461

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.671 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.527 AC: 80002 AN: 151776 Hom.: 21227 Cov.: 32

Gnomad AFR AF: 0.519

Gnomad AMI AF: 0.683

Gnomad AMR AF: 0.582

Gnomad ASJ AF: 0.529

Gnomad EAS AF: 0.690

Gnomad SAS AF: 0.545

Gnomad FIN AF: 0.494

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.509

Gnomad OTH AF: 0.534

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

GnomAD4 genome AF: 0.527 AC: 80042 AN: 151896 Hom.: 21234 Cov.: 32 AF XY: 0.526 AC XY: 39071 AN XY: 74222

Gnomad4 AFR AF: 0.519

Gnomad4 AMR AF: 0.582

Gnomad4 ASJ AF: 0.529

Gnomad4 EAS AF: 0.690

Gnomad4 SAS AF: 0.544

Gnomad4 FIN AF: 0.494

Gnomad4 NFE AF: 0.509

Gnomad4 OTH AF: 0.531

Alfa AF: 0.512 Hom.: 31364

Bravo AF: 0.536

Asia WGS AF: 0.575 AC: 2002 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.35
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6509940; hg19: chr19-55883879;