rs3015469

Variant names:

• chr14-50690442-G-A
• rs3015469

Your query was ambiguous. Multiple possible variants found:

• chr14-50690442-G-A
• chr14-50690442-G-C
• chr14-50690442-G-T

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 0.746 in 151,906 control chromosomes in the GnomAD database, including 42,589 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 0.75 (42589 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.617
• Publications: 10 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 (EAS) allele frequency at 95% confidence interval = 0.872 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: 0.746 AC: 113237 AN: 151788 Hom.: 42549 Cov.: 30

Gnomad AFR AF: 0.814

Gnomad AMI AF: 0.805

Gnomad AMR AF: 0.775

Gnomad ASJ AF: 0.705

Gnomad EAS AF: 0.893

Gnomad SAS AF: 0.706

Gnomad FIN AF: 0.722

Gnomad MID AF: 0.710

Gnomad NFE AF: 0.696

Gnomad OTH AF: 0.726

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

GnomAD4 genome AF: 0.746 AC: 113334 AN: 151906 Hom.: 42589 Cov.: 30 AF XY: 0.748 AC XY: 55493 AN XY: 74234

African (AFR) AF: 0.814 AC: 33719 AN: 41444

American (AMR) AF: 0.776 AC: 11842 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.705 AC: 2447 AN: 3470

East Asian (EAS) AF: 0.893 AC: 4615 AN: 5166

South Asian (SAS) AF: 0.705 AC: 3381 AN: 4796

European-Finnish (FIN) AF: 0.722 AC: 7603 AN: 10536

Middle Eastern (MID) AF: 0.702 AC: 205 AN: 292

European-Non Finnish (NFE) AF: 0.696 AC: 47257 AN: 67914

Other (OTH) AF: 0.727 AC: 1532 AN: 2108

Alfa AF: 0.709 Hom.: 117415

Bravo AF: 0.755

Asia WGS AF: 0.810 AC: 2794 AN: 3446

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.43
PhyloP100		-0.62

Splicing

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

Other links and lift over

dbSNP: rs3015469; hg19: chr14-51157160;