rs9600079

Variant names:

• chr13-73154002-G-T
• rs9600079

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 0.461 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.461 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

Gnomad4 AFR AF: 0.523

Gnomad4 AMR AF: 0.394

Gnomad4 ASJ AF: 0.436

Gnomad4 EAS AF: 0.447

Gnomad4 SAS AF: 0.467

Gnomad4 FIN AF: 0.415

Gnomad4 NFE AF: 0.448

Gnomad4 OTH AF: 0.457

Alfa AF: 0.446 Hom.: 34654

Bravo AF: 0.464

Asia WGS AF: 0.455 AC: 1584 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9600079; hg19: chr13-73728139;