rs6597604

Variant names:

• chr9-133174393-A-G
• rs6597604

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 0.259 in 152,146 control chromosomes in the GnomAD database, including 5,614 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 0.26 (5614 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.339

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.306 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: 0.260 AC: 39460 AN: 152028 Hom.: 5613 Cov.: 33

Gnomad AFR AF: 0.188

Gnomad AMI AF: 0.367

Gnomad AMR AF: 0.314

Gnomad ASJ AF: 0.239

Gnomad EAS AF: 0.00674

Gnomad SAS AF: 0.183

Gnomad FIN AF: 0.396

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.294

Gnomad OTH AF: 0.275

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

GnomAD4 genome AF: 0.259 AC: 39465 AN: 152146 Hom.: 5614 Cov.: 33 AF XY: 0.260 AC XY: 19364 AN XY: 74388

Gnomad4 AFR AF: 0.187

Gnomad4 AMR AF: 0.314

Gnomad4 ASJ AF: 0.239

Gnomad4 EAS AF: 0.00676

Gnomad4 SAS AF: 0.183

Gnomad4 FIN AF: 0.396

Gnomad4 NFE AF: 0.294

Gnomad4 OTH AF: 0.279

Alfa AF: 0.286 Hom.: 9742

Bravo AF: 0.252

Asia WGS AF: 0.110 AC: 381 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	4.3
DANN	Benign	0.19

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6597604; hg19: chr9-136049780;