chr19-39069167-A-C

Variant names:

• chr19-39069167-A-C
• rs576261

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 0.446 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
• Publications: 19 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.426 AC: 17573 AN: 41242

American (AMR) AF: 0.445 AC: 6729 AN: 15116

Ashkenazi Jewish (ASJ) AF: 0.435 AC: 1509 AN: 3466

East Asian (EAS) AF: 0.423 AC: 2170 AN: 5124

South Asian (SAS) AF: 0.405 AC: 1938 AN: 4780

European-Finnish (FIN) AF: 0.488 AC: 5097 AN: 10446

Middle Eastern (MID) AF: 0.429 AC: 126 AN: 294

European-Non Finnish (NFE) AF: 0.456 AC: 30933 AN: 67858

Other (OTH) AF: 0.455 AC: 958 AN: 2104

Alfa AF: 0.445 Hom.: 26441

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
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs576261; hg19: chr19-39559807;