rs9512645

Variant names:

• chr13-27356094-C-T
• rs9512645

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 0.15 in 152,256 control chromosomes in the GnomAD database, including 2,306 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 0.15 (2306 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.818

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 = 0.355 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: 0.151 AC: 22898 AN: 152138 Hom.: 2308 Cov.: 32

Gnomad AFR AF: 0.0386

Gnomad AMI AF: 0.265

Gnomad AMR AF: 0.129

Gnomad ASJ AF: 0.172

Gnomad EAS AF: 0.0371

Gnomad SAS AF: 0.369

Gnomad FIN AF: 0.108

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.220

Gnomad OTH AF: 0.162

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

GnomAD4 genome AF: 0.150 AC: 22897 AN: 152256 Hom.: 2306 Cov.: 32 AF XY: 0.147 AC XY: 10908 AN XY: 74438

Gnomad4 AFR AF: 0.0385

Gnomad4 AMR AF: 0.129

Gnomad4 ASJ AF: 0.172

Gnomad4 EAS AF: 0.0372

Gnomad4 SAS AF: 0.369

Gnomad4 FIN AF: 0.108

Gnomad4 NFE AF: 0.220

Gnomad4 OTH AF: 0.162

Alfa AF: 0.171 Hom.: 421

Bravo AF: 0.141

Asia WGS AF: 0.200 AC: 698 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	2.2
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9512645; hg19: chr13-27930231;