rs1409014

Variant names:

• chr13-49590426-G-A
• rs1409014

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 0.509 in 151,574 control chromosomes in the GnomAD database, including 20,576 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 0.51 (20576 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.188

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.617 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: 0.509 AC: 77083 AN: 151452 Hom.: 20552 Cov.: 32

Gnomad AFR AF: 0.376

Gnomad AMI AF: 0.424

Gnomad AMR AF: 0.539

Gnomad ASJ AF: 0.494

Gnomad EAS AF: 0.288

Gnomad SAS AF: 0.330

Gnomad FIN AF: 0.452

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.622

Gnomad OTH AF: 0.534

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

GnomAD4 genome AF: 0.509 AC: 77138 AN: 151574 Hom.: 20576 Cov.: 32 AF XY: 0.497 AC XY: 36789 AN XY: 74008

Gnomad4 AFR AF: 0.376

Gnomad4 AMR AF: 0.540

Gnomad4 ASJ AF: 0.494

Gnomad4 EAS AF: 0.288

Gnomad4 SAS AF: 0.331

Gnomad4 FIN AF: 0.452

Gnomad4 NFE AF: 0.622

Gnomad4 OTH AF: 0.536

Alfa AF: 0.557 Hom.: 2946

Bravo AF: 0.512

Asia WGS AF: 0.312 AC: 1087 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.1
DANN	Benign	0.20

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1409014; hg19: chr13-50164562;