rs1413334

Variant names:

• chr9-80304115-T-C
• rs1413334

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 0.296 in 152,130 control chromosomes in the GnomAD database, including 6,830 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 (6830 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.180
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.41 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.296 AC: 44950 AN: 152012 Hom.: 6822 Cov.: 33

Gnomad AFR AF: 0.292

Gnomad AMI AF: 0.394

Gnomad AMR AF: 0.301

Gnomad ASJ AF: 0.267

Gnomad EAS AF: 0.424

Gnomad SAS AF: 0.385

Gnomad FIN AF: 0.304

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.280

Gnomad OTH AF: 0.297

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

GnomAD4 genome AF: 0.296 AC: 44981 AN: 152130 Hom.: 6830 Cov.: 33 AF XY: 0.298 AC XY: 22186 AN XY: 74358

African (AFR) AF: 0.292 AC: 12104 AN: 41500

American (AMR) AF: 0.300 AC: 4592 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.267 AC: 927 AN: 3470

East Asian (EAS) AF: 0.425 AC: 2195 AN: 5170

South Asian (SAS) AF: 0.385 AC: 1856 AN: 4824

European-Finnish (FIN) AF: 0.304 AC: 3215 AN: 10574

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.280 AC: 19028 AN: 67980

Other (OTH) AF: 0.303 AC: 641 AN: 2114

Alfa AF: 0.293 Hom.: 3685

Bravo AF: 0.293

Asia WGS AF: 0.454 AC: 1578 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.3
DANN	Benign	0.42
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs1413334; hg19: chr9-82919030;