rs874966

Variant names:

• chr19-33298491-A-G
• rs874966

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 0.45 in 152,038 control chromosomes in the GnomAD database, including 15,550 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 (15550 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.571

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.512 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: 0.449 AC: 68268 AN: 151920 Hom.: 15515 Cov.: 33

Gnomad AFR AF: 0.517

Gnomad AMI AF: 0.570

Gnomad AMR AF: 0.383

Gnomad ASJ AF: 0.405

Gnomad EAS AF: 0.463

Gnomad SAS AF: 0.424

Gnomad FIN AF: 0.384

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.434

Gnomad OTH AF: 0.450

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

GnomAD4 genome AF: 0.450 AC: 68349 AN: 152038 Hom.: 15550 Cov.: 33 AF XY: 0.446 AC XY: 33137 AN XY: 74292

Gnomad4 AFR AF: 0.518

Gnomad4 AMR AF: 0.383

Gnomad4 ASJ AF: 0.405

Gnomad4 EAS AF: 0.464

Gnomad4 SAS AF: 0.427

Gnomad4 FIN AF: 0.384

Gnomad4 NFE AF: 0.435

Gnomad4 OTH AF: 0.446

Alfa AF: 0.450 Hom.: 4022

Bravo AF: 0.452

Asia WGS AF: 0.433 AC: 1508 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	11
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs874966; hg19: chr19-33789397;