rs1409014

Variant names:

• chr13-49590426-G-A
• rs1409014

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 0.509 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
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.376 AC: 15572 AN: 41396

American (AMR) AF: 0.540 AC: 8225 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.494 AC: 1710 AN: 3462

East Asian (EAS) AF: 0.288 AC: 1477 AN: 5136

South Asian (SAS) AF: 0.331 AC: 1596 AN: 4820

European-Finnish (FIN) AF: 0.452 AC: 4731 AN: 10466

Middle Eastern (MID) AF: 0.524 AC: 154 AN: 294

European-Non Finnish (NFE) AF: 0.622 AC: 42166 AN: 67756

Other (OTH) AF: 0.536 AC: 1128 AN: 2106

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.1
DANN	Benign	0.20
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs1409014; hg19: chr13-50164562;