rs3814333

Variant names:

• chr1-184037985-C-T
• rs3814333

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 0.287 in 152,044 control chromosomes in the GnomAD database, including 6,459 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 0.29 (6459 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.43

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.452 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: 0.288 AC: 43684 AN: 151926 Hom.: 6461 Cov.: 31

Gnomad AFR AF: 0.226

Gnomad AMI AF: 0.216

Gnomad AMR AF: 0.269

Gnomad ASJ AF: 0.200

Gnomad EAS AF: 0.468

Gnomad SAS AF: 0.296

Gnomad FIN AF: 0.367

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.309

Gnomad OTH AF: 0.265

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

GnomAD4 genome AF: 0.287 AC: 43704 AN: 152044 Hom.: 6459 Cov.: 31 AF XY: 0.290 AC XY: 21569 AN XY: 74296

Gnomad4 AFR AF: 0.226

Gnomad4 AMR AF: 0.269

Gnomad4 ASJ AF: 0.200

Gnomad4 EAS AF: 0.468

Gnomad4 SAS AF: 0.295

Gnomad4 FIN AF: 0.367

Gnomad4 NFE AF: 0.309

Gnomad4 OTH AF: 0.266

Alfa AF: 0.294 Hom.: 4067

Bravo AF: 0.280

Asia WGS AF: 0.357 AC: 1244 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.9
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3814333; hg19: chr1-184007119;