rs3899614

Variant names:

• chr3-14776220-G-A
• rs3899614

Your query was ambiguous. Multiple possible variants found:

• chr3-14776220-G-A
• chr3-14776220-G-C

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 0.539 in 152,088 control chromosomes in the GnomAD database, including 23,313 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 0.54 (23313 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.32
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.709 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.539 AC: 81866 AN: 151970 Hom.: 23282 Cov.: 33

Gnomad AFR AF: 0.716

Gnomad AMI AF: 0.537

Gnomad AMR AF: 0.592

Gnomad ASJ AF: 0.490

Gnomad EAS AF: 0.633

Gnomad SAS AF: 0.549

Gnomad FIN AF: 0.398

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.435

Gnomad OTH AF: 0.543

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

GnomAD4 genome AF: 0.539 AC: 81951 AN: 152088 Hom.: 23313 Cov.: 33 AF XY: 0.539 AC XY: 40090 AN XY: 74354

African (AFR) AF: 0.716 AC: 29689 AN: 41480

American (AMR) AF: 0.592 AC: 9042 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.490 AC: 1702 AN: 3470

East Asian (EAS) AF: 0.633 AC: 3279 AN: 5184

South Asian (SAS) AF: 0.547 AC: 2644 AN: 4832

European-Finnish (FIN) AF: 0.398 AC: 4200 AN: 10550

Middle Eastern (MID) AF: 0.588 AC: 173 AN: 294

European-Non Finnish (NFE) AF: 0.435 AC: 29577 AN: 67972

Other (OTH) AF: 0.547 AC: 1155 AN: 2112

Alfa AF: 0.473 Hom.: 40120

Bravo AF: 0.562

Asia WGS AF: 0.635 AC: 2212 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.34
DANN	Benign	0.26
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs3899614; hg19: chr3-14817727;