19-54028370-C-G

Variant names:

• chr19-54028370-C-G
• rs628604

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 0.53 in 150,728 control chromosomes in the GnomAD database, including 22,804 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 (22804 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.735 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: 0.530 AC: 79808 AN: 150616 Hom.: 22769 Cov.: 28

Gnomad AFR AF: 0.741

Gnomad AMI AF: 0.383

Gnomad AMR AF: 0.420

Gnomad ASJ AF: 0.434

Gnomad EAS AF: 0.706

Gnomad SAS AF: 0.583

Gnomad FIN AF: 0.428

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.433

Gnomad OTH AF: 0.517

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

GnomAD4 genome AF: 0.530 AC: 79888 AN: 150728 Hom.: 22804 Cov.: 28 AF XY: 0.529 AC XY: 38873 AN XY: 73512

Gnomad4 AFR AF: 0.741

Gnomad4 AMR AF: 0.420

Gnomad4 ASJ AF: 0.434

Gnomad4 EAS AF: 0.706

Gnomad4 SAS AF: 0.583

Gnomad4 FIN AF: 0.428

Gnomad4 NFE AF: 0.433

Gnomad4 OTH AF: 0.516

Alfa AF: 0.305 Hom.: 666

Bravo AF: 0.540

Asia WGS AF: 0.629 AC: 2187 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.065
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs628604; hg19: chr19-54531624;