19-54815284-T-C

Variant names:

• chr19-54815284-T-C
• rs581623

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 14 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.573 AC: 23210 AN: 40494

American (AMR) AF: 0.546 AC: 8215 AN: 15058

Ashkenazi Jewish (ASJ) AF: 0.434 AC: 1489 AN: 3432

East Asian (EAS) AF: 0.709 AC: 3624 AN: 5112

South Asian (SAS) AF: 0.463 AC: 2158 AN: 4664

European-Finnish (FIN) AF: 0.488 AC: 5066 AN: 10376

Middle Eastern (MID) AF: 0.395 AC: 116 AN: 294

European-Non Finnish (NFE) AF: 0.415 AC: 28083 AN: 67592

Other (OTH) AF: 0.479 AC: 996 AN: 2078

Alfa AF: 0.438 Hom.: 5368

Bravo AF: 0.506

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	5.0
DANN	Benign	0.24
PhyloP100		0.27
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs581623; hg19: chr19-55326739;