rs13288553

Variant names:

• chr9-84126546-G-T
• rs13288553

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 0.109 in 152,164 control chromosomes in the GnomAD database, including 1,163 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 (1163 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.587
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.162 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: 0.109 AC: 16530 AN: 152046 Hom.: 1159 Cov.: 32

Gnomad AFR AF: 0.0275

Gnomad AMI AF: 0.0559

Gnomad AMR AF: 0.0978

Gnomad ASJ AF: 0.163

Gnomad EAS AF: 0.0371

Gnomad SAS AF: 0.172

Gnomad FIN AF: 0.119

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.158

Gnomad OTH AF: 0.117

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

GnomAD4 genome AF: 0.109 AC: 16542 AN: 152164 Hom.: 1163 Cov.: 32 AF XY: 0.108 AC XY: 8000 AN XY: 74404

African (AFR) AF: 0.0275 AC: 1142 AN: 41536

American (AMR) AF: 0.0975 AC: 1491 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.163 AC: 567 AN: 3468

East Asian (EAS) AF: 0.0368 AC: 190 AN: 5166

South Asian (SAS) AF: 0.172 AC: 828 AN: 4816

European-Finnish (FIN) AF: 0.119 AC: 1263 AN: 10578

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.158 AC: 10716 AN: 67984

Other (OTH) AF: 0.122 AC: 258 AN: 2114

Alfa AF: 0.131 Hom.: 189

Bravo AF: 0.0983

Asia WGS AF: 0.111 AC: 384 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.7
DANN	Benign	0.73
PhyloP100		0.59

Splicing

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

Other links and lift over

dbSNP: rs13288553; hg19: chr9-86741461; COSMIC: COSV60369936;