rs576261

chr19-39069167-A-C

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 0.446 in 151,340 control chromosomes in the GnomAD database, including 15,061 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 0.45 (15061 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.357

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 (NFE) allele frequency at 95% confidence interval = 0.452 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: 0.446 AC: 67438 AN: 151222 Hom.: 15057 Cov.: 29

Gnomad AFR AF: 0.426

Gnomad AMI AF: 0.496

Gnomad AMR AF: 0.445

Gnomad ASJ AF: 0.435

Gnomad EAS AF: 0.423

Gnomad SAS AF: 0.405

Gnomad FIN AF: 0.488

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.456

Gnomad OTH AF: 0.457

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

GnomAD4 genome AF: 0.446 AC: 67484 AN: 151340 Hom.: 15061 Cov.: 29 AF XY: 0.447 AC XY: 33013 AN XY: 73896

Gnomad4 AFR AF: 0.426

Gnomad4 AMR AF: 0.445

Gnomad4 ASJ AF: 0.435

Gnomad4 EAS AF: 0.423

Gnomad4 SAS AF: 0.405

Gnomad4 FIN AF: 0.488

Gnomad4 NFE AF: 0.456

Gnomad4 OTH AF: 0.455

Alfa AF: 0.446 Hom.: 17096

Bravo AF: 0.443

Asia WGS AF: 0.440 AC: 1532 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.8
Dann	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs576261; hg19: chr19-39559807;