rs874966

Variant names:

• chr19-33298491-A-G
• rs874966

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 0.45 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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.518 AC: 21469 AN: 41476

American (AMR) AF: 0.383 AC: 5848 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.405 AC: 1407 AN: 3470

East Asian (EAS) AF: 0.464 AC: 2388 AN: 5152

South Asian (SAS) AF: 0.427 AC: 2060 AN: 4826

European-Finnish (FIN) AF: 0.384 AC: 4067 AN: 10580

Middle Eastern (MID) AF: 0.449 AC: 132 AN: 294

European-Non Finnish (NFE) AF: 0.435 AC: 29516 AN: 67926

Other (OTH) AF: 0.446 AC: 942 AN: 2114

Alfa AF: 0.448 Hom.: 26831

Bravo AF: 0.452

Asia WGS AF: 0.433 AC: 1508 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	11
DANN	Benign	0.68
PhyloP100		0.57

Splicing

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

Other links and lift over

dbSNP: rs874966; hg19: chr19-33789397;