rs9598783

Positions:

• chr13-64371042-C-G

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 0.43 in 151,908 control chromosomes in the GnomAD database, including 14,456 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 0.43 (14456 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.20

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.513 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.430 AC: 65211 AN: 151790 Hom.: 14430 Cov.: 31

Gnomad AFR AF: 0.413

Gnomad AMI AF: 0.542

Gnomad AMR AF: 0.522

Gnomad ASJ AF: 0.411

Gnomad EAS AF: 0.236

Gnomad SAS AF: 0.390

Gnomad FIN AF: 0.307

Gnomad MID AF: 0.347

Gnomad NFE AF: 0.455

Gnomad OTH AF: 0.433

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

GnomAD4 genome AF: 0.430 AC: 65291 AN: 151908 Hom.: 14456 Cov.: 31 AF XY: 0.425 AC XY: 31548 AN XY: 74218

Gnomad4 AFR AF: 0.414

Gnomad4 AMR AF: 0.523

Gnomad4 ASJ AF: 0.411

Gnomad4 EAS AF: 0.237

Gnomad4 SAS AF: 0.390

Gnomad4 FIN AF: 0.307

Gnomad4 NFE AF: 0.455

Gnomad4 OTH AF: 0.436

Alfa AF: 0.451 Hom.: 1961

Bravo AF: 0.445

Asia WGS AF: 0.372 AC: 1293 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.4
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9598783; hg19: chr13-64945174;