rs3899614

chr3-14776220-G-Achr3-14776220-G-C

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 0.539 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.716

Gnomad4 AMR AF: 0.592

Gnomad4 ASJ AF: 0.490

Gnomad4 EAS AF: 0.633

Gnomad4 SAS AF: 0.547

Gnomad4 FIN AF: 0.398

Gnomad4 NFE AF: 0.435

Gnomad4 OTH AF: 0.547

Alfa AF: 0.466 Hom.: 24709

Bravo AF: 0.562

Asia WGS AF: 0.635 AC: 2212 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.34
Dann	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3899614; hg19: chr3-14817727;