rs1333404

Variant names:

• chr13-81167696-A-G
• rs1333404

Your query was ambiguous. Multiple possible variants found:

• chr13-81167696-A-G
• chr13-81167696-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 0.226 in 152,140 control chromosomes in the GnomAD database, including 3,940 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 0.23 (3940 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.497

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.314 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: 0.226 AC: 34327 AN: 152022 Hom.: 3934 Cov.: 33

Gnomad AFR AF: 0.240

Gnomad AMI AF: 0.255

Gnomad AMR AF: 0.184

Gnomad ASJ AF: 0.290

Gnomad EAS AF: 0.222

Gnomad SAS AF: 0.329

Gnomad FIN AF: 0.263

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.211

Gnomad OTH AF: 0.204

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

GnomAD4 genome AF: 0.226 AC: 34351 AN: 152140 Hom.: 3940 Cov.: 33 AF XY: 0.230 AC XY: 17101 AN XY: 74384

Gnomad4 AFR AF: 0.240

Gnomad4 AMR AF: 0.184

Gnomad4 ASJ AF: 0.290

Gnomad4 EAS AF: 0.222

Gnomad4 SAS AF: 0.328

Gnomad4 FIN AF: 0.263

Gnomad4 NFE AF: 0.211

Gnomad4 OTH AF: 0.208

Alfa AF: 0.216 Hom.: 7295

Bravo AF: 0.218

Asia WGS AF: 0.301 AC: 1044 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.6
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1333404; hg19: chr13-81741831;