rs688187

chr19-39242112-G-A

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 0.387 in 150,696 control chromosomes in the GnomAD database, including 12,992 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 0.39 (12992 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.342

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.6 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.386 AC: 58199 AN: 150580 Hom.: 12960 Cov.: 31

Gnomad AFR AF: 0.606

Gnomad AMI AF: 0.370

Gnomad AMR AF: 0.373

Gnomad ASJ AF: 0.388

Gnomad EAS AF: 0.0711

Gnomad SAS AF: 0.218

Gnomad FIN AF: 0.238

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.318

Gnomad OTH AF: 0.363

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

GnomAD4 genome AF: 0.387 AC: 58279 AN: 150696 Hom.: 12992 Cov.: 31 AF XY: 0.377 AC XY: 27743 AN XY: 73628

Gnomad4 AFR AF: 0.606

Gnomad4 AMR AF: 0.372

Gnomad4 ASJ AF: 0.388

Gnomad4 EAS AF: 0.0715

Gnomad4 SAS AF: 0.218

Gnomad4 FIN AF: 0.238

Gnomad4 NFE AF: 0.318

Gnomad4 OTH AF: 0.359

Alfa AF: 0.372 Hom.: 1373

Bravo AF: 0.409

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.4
Dann	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs688187; hg19: chr19-39732752;