rs9600079

Variant names:

• chr13-73154002-G-T
• rs9600079

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 0.461 in 152,048 control chromosomes in the GnomAD database, including 16,322 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 0.46 (16322 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0320
• Publications: 63 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.517 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: 0.461 AC: 70103 AN: 151930 Hom.: 16306 Cov.: 32

Gnomad AFR AF: 0.523

Gnomad AMI AF: 0.445

Gnomad AMR AF: 0.395

Gnomad ASJ AF: 0.436

Gnomad EAS AF: 0.447

Gnomad SAS AF: 0.465

Gnomad FIN AF: 0.415

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.448

Gnomad OTH AF: 0.462

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

GnomAD4 genome AF: 0.461 AC: 70146 AN: 152048 Hom.: 16322 Cov.: 32 AF XY: 0.458 AC XY: 34031 AN XY: 74322

African (AFR) AF: 0.523 AC: 21683 AN: 41470

American (AMR) AF: 0.394 AC: 6026 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.436 AC: 1512 AN: 3464

East Asian (EAS) AF: 0.447 AC: 2312 AN: 5170

South Asian (SAS) AF: 0.467 AC: 2250 AN: 4820

European-Finnish (FIN) AF: 0.415 AC: 4387 AN: 10562

Middle Eastern (MID) AF: 0.439 AC: 129 AN: 294

European-Non Finnish (NFE) AF: 0.448 AC: 30476 AN: 67966

Other (OTH) AF: 0.457 AC: 965 AN: 2110

Alfa AF: 0.450 Hom.: 69401

Bravo AF: 0.464

Asia WGS AF: 0.455 AC: 1584 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.5
DANN	Benign	0.30
PhyloP100		-0.032

Splicing

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

Other links and lift over

dbSNP: rs9600079; hg19: chr13-73728139;