rs1359679

Variant names:

• chr9-118835336-T-C
• rs1359679

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.436 AC: 18051 AN: 41404

American (AMR) AF: 0.277 AC: 4228 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.242 AC: 839 AN: 3472

East Asian (EAS) AF: 0.484 AC: 2493 AN: 5152

South Asian (SAS) AF: 0.347 AC: 1673 AN: 4818

European-Finnish (FIN) AF: 0.296 AC: 3129 AN: 10554

Middle Eastern (MID) AF: 0.284 AC: 83 AN: 292

European-Non Finnish (NFE) AF: 0.250 AC: 16964 AN: 67938

Other (OTH) AF: 0.317 AC: 671 AN: 2116

Alfa AF: 0.275 Hom.: 18726

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
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs1359679; hg19: chr9-121597614;