19-54815284-T-C

Variant names:

• chr19-54815284-T-C
• rs581623

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 0.489 in 150,002 control chromosomes in the GnomAD database, including 19,045 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 0.49 (19045 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.267

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.69 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: 0.489 AC: 73223 AN: 149884 Hom.: 19011 Cov.: 30

Gnomad AFR AF: 0.573

Gnomad AMI AF: 0.379

Gnomad AMR AF: 0.545

Gnomad ASJ AF: 0.434

Gnomad EAS AF: 0.709

Gnomad SAS AF: 0.465

Gnomad FIN AF: 0.488

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.415

Gnomad OTH AF: 0.479

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

GnomAD4 genome AF: 0.489 AC: 73299 AN: 150002 Hom.: 19045 Cov.: 30 AF XY: 0.497 AC XY: 36417 AN XY: 73222

Gnomad4 AFR AF: 0.573

Gnomad4 AMR AF: 0.546

Gnomad4 ASJ AF: 0.434

Gnomad4 EAS AF: 0.709

Gnomad4 SAS AF: 0.463

Gnomad4 FIN AF: 0.488

Gnomad4 NFE AF: 0.415

Gnomad4 OTH AF: 0.479

Alfa AF: 0.437 Hom.: 3548

Bravo AF: 0.506

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	5.0
DANN	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs581623; hg19: chr19-55326739;