rs1359679

Variant names:

• chr9-118835336-T-C
• rs1359679

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 0.318 in 151,904 control chromosomes in the GnomAD database, including 8,319 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 0.32 (8319 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.38

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.468 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: 0.317 AC: 48158 AN: 151786 Hom.: 8273 Cov.: 32

Gnomad AFR AF: 0.435

Gnomad AMI AF: 0.134

Gnomad AMR AF: 0.277

Gnomad ASJ AF: 0.242

Gnomad EAS AF: 0.484

Gnomad SAS AF: 0.348

Gnomad FIN AF: 0.296

Gnomad MID AF: 0.283

Gnomad NFE AF: 0.250

Gnomad OTH AF: 0.311

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

GnomAD4 genome AF: 0.318 AC: 48253 AN: 151904 Hom.: 8319 Cov.: 32 AF XY: 0.322 AC XY: 23907 AN XY: 74212

Gnomad4 AFR AF: 0.436

Gnomad4 AMR AF: 0.277

Gnomad4 ASJ AF: 0.242

Gnomad4 EAS AF: 0.484

Gnomad4 SAS AF: 0.347

Gnomad4 FIN AF: 0.296

Gnomad4 NFE AF: 0.250

Gnomad4 OTH AF: 0.317

Alfa AF: 0.264 Hom.: 10905

Bravo AF: 0.321

Asia WGS AF: 0.435 AC: 1505 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.051
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1359679; hg19: chr9-121597614;