rs9603665

chr13-40028210-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 0.304 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;