rs1413280

Variant names:

• chr13-88023507-A-C
• rs1413280

Your query was ambiguous. Multiple possible variants found:

• chr13-88023507-A-C
• chr13-88023507-A-G
• chr13-88023507-A-T

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 0.471 in 151,562 control chromosomes in the GnomAD database, including 19,083 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 0.47 (19083 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -9.15

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.15).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.734 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: 0.471 AC: 71266 AN: 151444 Hom.: 19057 Cov.: 31

Gnomad AFR AF: 0.741

Gnomad AMI AF: 0.271

Gnomad AMR AF: 0.366

Gnomad ASJ AF: 0.479

Gnomad EAS AF: 0.352

Gnomad SAS AF: 0.527

Gnomad FIN AF: 0.339

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.357

Gnomad OTH AF: 0.458

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

GnomAD4 genome AF: 0.471 AC: 71329 AN: 151562 Hom.: 19083 Cov.: 31 AF XY: 0.469 AC XY: 34717 AN XY: 74062

Gnomad4 AFR AF: 0.741

Gnomad4 AMR AF: 0.365

Gnomad4 ASJ AF: 0.479

Gnomad4 EAS AF: 0.352

Gnomad4 SAS AF: 0.527

Gnomad4 FIN AF: 0.339

Gnomad4 NFE AF: 0.357

Gnomad4 OTH AF: 0.456

Alfa AF: 0.254 Hom.: 586

Bravo AF: 0.481

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.0030
DANN	Benign	0.23

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1413280; hg19: chr13-88675762;