3-189930300-C-T

Variant names:

• chr3-189930300-C-T
• rs1515504

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 0.379 in 151,890 control chromosomes in the GnomAD database, including 11,230 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 0.38 (11230 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.189
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.459 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: 0.379 AC: 57523 AN: 151772 Hom.: 11214 Cov.: 32

Gnomad AFR AF: 0.422

Gnomad AMI AF: 0.292

Gnomad AMR AF: 0.467

Gnomad ASJ AF: 0.290

Gnomad EAS AF: 0.424

Gnomad SAS AF: 0.334

Gnomad FIN AF: 0.476

Gnomad MID AF: 0.306

Gnomad NFE AF: 0.324

Gnomad OTH AF: 0.361

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

GnomAD4 genome AF: 0.379 AC: 57590 AN: 151890 Hom.: 11230 Cov.: 32 AF XY: 0.386 AC XY: 28671 AN XY: 74232

African (AFR) AF: 0.422 AC: 17498 AN: 41454

American (AMR) AF: 0.468 AC: 7126 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.290 AC: 1007 AN: 3468

East Asian (EAS) AF: 0.423 AC: 2182 AN: 5156

South Asian (SAS) AF: 0.334 AC: 1607 AN: 4816

European-Finnish (FIN) AF: 0.476 AC: 5034 AN: 10568

Middle Eastern (MID) AF: 0.305 AC: 89 AN: 292

European-Non Finnish (NFE) AF: 0.324 AC: 22024 AN: 67904

Other (OTH) AF: 0.360 AC: 758 AN: 2104

Alfa AF: 0.362 Hom.: 4072

Bravo AF: 0.381

Asia WGS AF: 0.358 AC: 1240 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	1.8
DANN	Benign	0.68
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs1515504; hg19: chr3-189648089;