rs1409014

chr13-49590426-G-A

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;