rs878246

Variant names:

• chr19-9193409-T-C
• rs878246

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 0.225 in 152,144 control chromosomes in the GnomAD database, including 3,957 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 0.22 (3957 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.247

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.261 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: 0.225 AC: 34217 AN: 152026 Hom.: 3961 Cov.: 32

Gnomad AFR AF: 0.219

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.180

Gnomad ASJ AF: 0.281

Gnomad EAS AF: 0.255

Gnomad SAS AF: 0.273

Gnomad FIN AF: 0.271

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.223

Gnomad OTH AF: 0.243

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

GnomAD4 genome AF: 0.225 AC: 34216 AN: 152144 Hom.: 3957 Cov.: 32 AF XY: 0.228 AC XY: 16963 AN XY: 74364

Gnomad4 AFR AF: 0.218

Gnomad4 AMR AF: 0.180

Gnomad4 ASJ AF: 0.281

Gnomad4 EAS AF: 0.255

Gnomad4 SAS AF: 0.273

Gnomad4 FIN AF: 0.271

Gnomad4 NFE AF: 0.223

Gnomad4 OTH AF: 0.245

Alfa AF: 0.224 Hom.: 1211

Bravo AF: 0.215

Asia WGS AF: 0.253 AC: 880 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.2
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs878246; hg19: chr19-9304085;