rs9512645

Positions:

• chr13-27356094-C-T

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;