chr19-29882485-C-A

Variant names:

• chr19-29882485-C-A
• rs335016

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 0.412 in 151,946 control chromosomes in the GnomAD database, including 12,975 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 0.41 (12975 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.972

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.471 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: 0.412 AC: 62529 AN: 151828 Hom.: 12958 Cov.: 32

Gnomad AFR AF: 0.385

Gnomad AMI AF: 0.295

Gnomad AMR AF: 0.444

Gnomad ASJ AF: 0.382

Gnomad EAS AF: 0.422

Gnomad SAS AF: 0.488

Gnomad FIN AF: 0.481

Gnomad MID AF: 0.293

Gnomad NFE AF: 0.408

Gnomad OTH AF: 0.409

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

GnomAD4 genome AF: 0.412 AC: 62593 AN: 151946 Hom.: 12975 Cov.: 32 AF XY: 0.416 AC XY: 30889 AN XY: 74232

Gnomad4 AFR AF: 0.385

Gnomad4 AMR AF: 0.445

Gnomad4 ASJ AF: 0.382

Gnomad4 EAS AF: 0.421

Gnomad4 SAS AF: 0.488

Gnomad4 FIN AF: 0.481

Gnomad4 NFE AF: 0.408

Gnomad4 OTH AF: 0.407

Alfa AF: 0.272 Hom.: 644

Bravo AF: 0.410

Asia WGS AF: 0.424 AC: 1476 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.34
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs335016; hg19: chr19-30373392;