rs930100

Variant names:

• chr19-39053594-G-T
• rs930100

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 0.288 in 152,040 control chromosomes in the GnomAD database, including 6,616 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 0.29 (6616 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.539

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.483 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: 0.288 AC: 43727 AN: 151922 Hom.: 6599 Cov.: 32

Gnomad AFR AF: 0.220

Gnomad AMI AF: 0.262

Gnomad AMR AF: 0.321

Gnomad ASJ AF: 0.327

Gnomad EAS AF: 0.382

Gnomad SAS AF: 0.499

Gnomad FIN AF: 0.312

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.294

Gnomad OTH AF: 0.283

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

GnomAD4 genome AF: 0.288 AC: 43781 AN: 152040 Hom.: 6616 Cov.: 32 AF XY: 0.294 AC XY: 21847 AN XY: 74296

Gnomad4 AFR AF: 0.221

Gnomad4 AMR AF: 0.322

Gnomad4 ASJ AF: 0.327

Gnomad4 EAS AF: 0.382

Gnomad4 SAS AF: 0.500

Gnomad4 FIN AF: 0.312

Gnomad4 NFE AF: 0.294

Gnomad4 OTH AF: 0.283

Alfa AF: 0.307 Hom.: 3589

Bravo AF: 0.280

Asia WGS AF: 0.405 AC: 1407 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.7
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: rs930100; hg19: chr19-39544234;