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. The variant received -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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.240 AC: 9942 AN: 41508

American (AMR) AF: 0.184 AC: 2810 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.290 AC: 1005 AN: 3466

East Asian (EAS) AF: 0.222 AC: 1147 AN: 5166

South Asian (SAS) AF: 0.328 AC: 1579 AN: 4816

European-Finnish (FIN) AF: 0.263 AC: 2783 AN: 10578

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.211 AC: 14330 AN: 67992

Other (OTH) AF: 0.208 AC: 440 AN: 2112

Alfa AF: 0.217 Hom.: 11298

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
PhyloP100		0.50

Splicing

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

Other links and lift over

dbSNP: rs1333404; hg19: chr13-81741831;