rs1328406

Variant names:

• chr9-79342883-C-T
• rs1328406

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 0.297 in 151,980 control chromosomes in the GnomAD database, including 6,826 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 (6826 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.462
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.346 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.297 AC: 45144 AN: 151862 Hom.: 6810 Cov.: 32

Gnomad AFR AF: 0.318

Gnomad AMI AF: 0.360

Gnomad AMR AF: 0.305

Gnomad ASJ AF: 0.232

Gnomad EAS AF: 0.361

Gnomad SAS AF: 0.348

Gnomad FIN AF: 0.320

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.274

Gnomad OTH AF: 0.289

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

GnomAD4 genome AF: 0.297 AC: 45176 AN: 151980 Hom.: 6826 Cov.: 32 AF XY: 0.300 AC XY: 22265 AN XY: 74274

African (AFR) AF: 0.318 AC: 13163 AN: 41428

American (AMR) AF: 0.306 AC: 4679 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.232 AC: 804 AN: 3470

East Asian (EAS) AF: 0.360 AC: 1862 AN: 5174

South Asian (SAS) AF: 0.347 AC: 1673 AN: 4816

European-Finnish (FIN) AF: 0.320 AC: 3373 AN: 10532

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.274 AC: 18616 AN: 67966

Other (OTH) AF: 0.290 AC: 612 AN: 2110

Alfa AF: 0.287 Hom.: 9937

Bravo AF: 0.300

Asia WGS AF: 0.369 AC: 1286 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.4
DANN	Benign	0.60
PhyloP100		0.46

Splicing

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

Other links and lift over

dbSNP: rs1328406; hg19: chr9-81957798;