rs17796312

Variant names:

• chr19-39852835-A-G
• rs17796312

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 0.302 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.302 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

Gnomad4 AFR AF: 0.194

Gnomad4 AMR AF: 0.283

Gnomad4 ASJ AF: 0.248

Gnomad4 EAS AF: 0.557

Gnomad4 SAS AF: 0.423

Gnomad4 FIN AF: 0.336

Gnomad4 NFE AF: 0.339

Gnomad4 OTH AF: 0.317

Alfa AF: 0.322 Hom.: 1957

Bravo AF: 0.295

Asia WGS AF: 0.426 AC: 1480 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17796312; hg19: chr19-40343475;