rs3814333

Variant names:

• chr1-184037985-C-T
• rs3814333

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 0.287 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
• Publications: 29 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.226 AC: 9355 AN: 41482

American (AMR) AF: 0.269 AC: 4111 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.200 AC: 693 AN: 3470

East Asian (EAS) AF: 0.468 AC: 2415 AN: 5164

South Asian (SAS) AF: 0.295 AC: 1420 AN: 4812

European-Finnish (FIN) AF: 0.367 AC: 3867 AN: 10548

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.309 AC: 21005 AN: 67968

Other (OTH) AF: 0.266 AC: 561 AN: 2112

Alfa AF: 0.300 Hom.: 16317

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
PhyloP100		-1.4
PromoterAI		0.0097	Neutral

Splicing

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

Other links and lift over

dbSNP: rs3814333; hg19: chr1-184007119;