rs1409504

Variant names:

• chr13-30129502-G-A
• rs1409504

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 0.112 in 152,202 control chromosomes in the GnomAD database, including 1,503 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 0.11 (1503 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.274
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.251 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: 0.112 AC: 17044 AN: 152084 Hom.: 1496 Cov.: 32

Gnomad AFR AF: 0.255

Gnomad AMI AF: 0.0285

Gnomad AMR AF: 0.0620

Gnomad ASJ AF: 0.0516

Gnomad EAS AF: 0.0381

Gnomad SAS AF: 0.0672

Gnomad FIN AF: 0.0357

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.0620

Gnomad OTH AF: 0.0845

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

GnomAD4 genome AF: 0.112 AC: 17077 AN: 152202 Hom.: 1503 Cov.: 32 AF XY: 0.109 AC XY: 8087 AN XY: 74408

African (AFR) AF: 0.255 AC: 10584 AN: 41460

American (AMR) AF: 0.0620 AC: 948 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0516 AC: 179 AN: 3472

East Asian (EAS) AF: 0.0382 AC: 198 AN: 5188

South Asian (SAS) AF: 0.0681 AC: 329 AN: 4832

European-Finnish (FIN) AF: 0.0357 AC: 379 AN: 10606

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.0620 AC: 4218 AN: 68022

Other (OTH) AF: 0.0832 AC: 176 AN: 2116

Alfa AF: 0.0747 Hom.: 1028

Bravo AF: 0.120

Asia WGS AF: 0.0620 AC: 215 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.0
DANN	Benign	0.18
PhyloP100		0.27

Splicing

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

Other links and lift over

dbSNP: rs1409504; hg19: chr13-30703639;