rs33925946

Variant names:

• chr14-104805499-G-T
• rs33925946

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 0.271 in 152,114 control chromosomes in the GnomAD database, including 5,828 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 0.27 (5828 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.102
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.286 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: 0.271 AC: 41232 AN: 151992 Hom.: 5822 Cov.: 33

Gnomad AFR AF: 0.290

Gnomad AMI AF: 0.273

Gnomad AMR AF: 0.234

Gnomad ASJ AF: 0.252

Gnomad EAS AF: 0.109

Gnomad SAS AF: 0.176

Gnomad FIN AF: 0.293

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.286

Gnomad OTH AF: 0.261

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

GnomAD4 genome AF: 0.271 AC: 41275 AN: 152114 Hom.: 5828 Cov.: 33 AF XY: 0.269 AC XY: 19991 AN XY: 74348

African (AFR) AF: 0.290 AC: 12049 AN: 41496

American (AMR) AF: 0.234 AC: 3572 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.252 AC: 875 AN: 3468

East Asian (EAS) AF: 0.109 AC: 566 AN: 5170

South Asian (SAS) AF: 0.177 AC: 854 AN: 4822

European-Finnish (FIN) AF: 0.293 AC: 3099 AN: 10580

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.286 AC: 19406 AN: 67962

Other (OTH) AF: 0.262 AC: 555 AN: 2116

Alfa AF: 0.281 Hom.: 8253

Bravo AF: 0.270

Asia WGS AF: 0.134 AC: 464 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	8.0
DANN	Benign	0.87
PhyloP100		0.10

Splicing

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

Other links and lift over

dbSNP: rs33925946; hg19: chr14-105271836; COSMIC: COSV61137009;