rs1359679

Positions:

• chr9-118835336-T-C

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;