rs13332653

Variant names:

• chr16-24578078-T-G
• rs13332653

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 0.114 in 152,294 control chromosomes in the GnomAD database, including 1,044 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 (1044 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.369

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.132 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: 0.114 AC: 17417 AN: 152176 Hom.: 1046 Cov.: 32

Gnomad AFR AF: 0.0888

Gnomad AMI AF: 0.115

Gnomad AMR AF: 0.116

Gnomad ASJ AF: 0.0827

Gnomad EAS AF: 0.0786

Gnomad SAS AF: 0.142

Gnomad FIN AF: 0.108

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.132

Gnomad OTH AF: 0.139

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

GnomAD4 genome AF: 0.114 AC: 17418 AN: 152294 Hom.: 1044 Cov.: 32 AF XY: 0.115 AC XY: 8580 AN XY: 74464

Gnomad4 AFR AF: 0.0889

Gnomad4 AMR AF: 0.116

Gnomad4 ASJ AF: 0.0827

Gnomad4 EAS AF: 0.0786

Gnomad4 SAS AF: 0.141

Gnomad4 FIN AF: 0.108

Gnomad4 NFE AF: 0.132

Gnomad4 OTH AF: 0.137

Alfa AF: 0.128 Hom.: 1295

Bravo AF: 0.114

Asia WGS AF: 0.104 AC: 362 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	6.8
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13332653; hg19: chr16-24589399;