chr19-39852835-A-G

Variant names:

• chr19-39852835-A-G
• rs17796312

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 0.302 in 152,092 control chromosomes in the GnomAD database, including 7,481 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 0.30 (7481 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.131
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.54 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.302 AC: 45927 AN: 151974 Hom.: 7477 Cov.: 31

Gnomad AFR AF: 0.194

Gnomad AMI AF: 0.464

Gnomad AMR AF: 0.282

Gnomad ASJ AF: 0.248

Gnomad EAS AF: 0.556

Gnomad SAS AF: 0.424

Gnomad FIN AF: 0.336

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.339

Gnomad OTH AF: 0.317

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

GnomAD4 genome AF: 0.302 AC: 45942 AN: 152092 Hom.: 7481 Cov.: 31 AF XY: 0.304 AC XY: 22576 AN XY: 74344

African (AFR) AF: 0.194 AC: 8054 AN: 41498

American (AMR) AF: 0.283 AC: 4311 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.248 AC: 859 AN: 3470

East Asian (EAS) AF: 0.557 AC: 2876 AN: 5168

South Asian (SAS) AF: 0.423 AC: 2044 AN: 4828

European-Finnish (FIN) AF: 0.336 AC: 3546 AN: 10568

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.339 AC: 23073 AN: 67988

Other (OTH) AF: 0.317 AC: 670 AN: 2112

Alfa AF: 0.326 Hom.: 3509

Bravo AF: 0.295

Asia WGS AF: 0.426 AC: 1480 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	10
DANN	Benign	0.87
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs17796312; hg19: chr19-40343475;