rs373409

Variant names:

• chr14-45874286-G-A
• rs373409

Your query was ambiguous. Multiple possible variants found:

• chr14-45874286-G-A
• chr14-45874286-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 0.699 in 152,006 control chromosomes in the GnomAD database, including 37,914 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 0.70 (37914 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.906 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: 0.699 AC: 106189 AN: 151888 Hom.: 37892 Cov.: 31

Gnomad AFR AF: 0.552

Gnomad AMI AF: 0.652

Gnomad AMR AF: 0.740

Gnomad ASJ AF: 0.658

Gnomad EAS AF: 0.928

Gnomad SAS AF: 0.802

Gnomad FIN AF: 0.745

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.750

Gnomad OTH AF: 0.715

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

GnomAD4 genome AF: 0.699 AC: 106265 AN: 152006 Hom.: 37914 Cov.: 31 AF XY: 0.702 AC XY: 52129 AN XY: 74286

African (AFR) AF: 0.552 AC: 22865 AN: 41424

American (AMR) AF: 0.741 AC: 11331 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.658 AC: 2284 AN: 3472

East Asian (EAS) AF: 0.928 AC: 4777 AN: 5146

South Asian (SAS) AF: 0.802 AC: 3863 AN: 4818

European-Finnish (FIN) AF: 0.745 AC: 7884 AN: 10576

Middle Eastern (MID) AF: 0.609 AC: 179 AN: 294

European-Non Finnish (NFE) AF: 0.750 AC: 50986 AN: 67970

Other (OTH) AF: 0.714 AC: 1503 AN: 2106

Alfa AF: 0.721 Hom.: 5204

Bravo AF: 0.694

Asia WGS AF: 0.823 AC: 2860 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	5.2
DANN	Benign	0.63
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs373409; hg19: chr14-46343489;