rs9603665

Variant names:

• chr13-40028210-C-T
• rs9603665

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 0.304 in 152,048 control chromosomes in the GnomAD database, including 7,697 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 0.30 (7697 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.406

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.385 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: 0.304 AC: 46185 AN: 151930 Hom.: 7695 Cov.: 31

Gnomad AFR AF: 0.177

Gnomad AMI AF: 0.434

Gnomad AMR AF: 0.393

Gnomad ASJ AF: 0.285

Gnomad EAS AF: 0.187

Gnomad SAS AF: 0.223

Gnomad FIN AF: 0.352

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.368

Gnomad OTH AF: 0.297

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

GnomAD4 genome AF: 0.304 AC: 46190 AN: 152048 Hom.: 7697 Cov.: 31 AF XY: 0.301 AC XY: 22398 AN XY: 74328

Gnomad4 AFR AF: 0.177

Gnomad4 AMR AF: 0.394

Gnomad4 ASJ AF: 0.285

Gnomad4 EAS AF: 0.187

Gnomad4 SAS AF: 0.222

Gnomad4 FIN AF: 0.352

Gnomad4 NFE AF: 0.368

Gnomad4 OTH AF: 0.292

Alfa AF: 0.352 Hom.: 12985

Bravo AF: 0.305

Asia WGS AF: 0.195 AC: 678 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.23
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9603665; hg19: chr13-40602347;