13-33084771-A-G

Variant names:

• chr13-33084771-A-G
• rs809991

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 0.933 in 152,212 control chromosomes in the GnomAD database, including 66,352 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 0.93 (66352 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.898

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 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: 0.933 AC: 141960 AN: 152094 Hom.: 66287 Cov.: 32

Gnomad AFR AF: 0.944

Gnomad AMI AF: 0.944

Gnomad AMR AF: 0.954

Gnomad ASJ AF: 0.850

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.884

Gnomad FIN AF: 0.900

Gnomad MID AF: 0.915

Gnomad NFE AF: 0.930

Gnomad OTH AF: 0.941

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

GnomAD4 genome AF: 0.933 AC: 142083 AN: 152212 Hom.: 66352 Cov.: 32 AF XY: 0.932 AC XY: 69392 AN XY: 74416

Gnomad4 AFR AF: 0.944

Gnomad4 AMR AF: 0.954

Gnomad4 ASJ AF: 0.850

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.883

Gnomad4 FIN AF: 0.900

Gnomad4 NFE AF: 0.930

Gnomad4 OTH AF: 0.942

Alfa AF: 0.930 Hom.: 12769

Bravo AF: 0.940

Asia WGS AF: 0.957 AC: 3312 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	7.2
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs809991; hg19: chr13-33658908;