rs959898

Variant names:

• chr13-93084596-C-T
• rs959898

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 0.495 in 152,028 control chromosomes in the GnomAD database, including 19,858 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 0.50 (19858 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.678 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: 0.495 AC: 75245 AN: 151910 Hom.: 19848 Cov.: 32

Gnomad AFR AF: 0.302

Gnomad AMI AF: 0.465

Gnomad AMR AF: 0.600

Gnomad ASJ AF: 0.587

Gnomad EAS AF: 0.674

Gnomad SAS AF: 0.699

Gnomad FIN AF: 0.554

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.546

Gnomad OTH AF: 0.536

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

GnomAD4 genome AF: 0.495 AC: 75285 AN: 152028 Hom.: 19858 Cov.: 32 AF XY: 0.501 AC XY: 37239 AN XY: 74302

Gnomad4 AFR AF: 0.302

Gnomad4 AMR AF: 0.601

Gnomad4 ASJ AF: 0.587

Gnomad4 EAS AF: 0.674

Gnomad4 SAS AF: 0.698

Gnomad4 FIN AF: 0.554

Gnomad4 NFE AF: 0.546

Gnomad4 OTH AF: 0.541

Alfa AF: 0.509 Hom.: 5162

Bravo AF: 0.488

Asia WGS AF: 0.689 AC: 2394 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.059
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs959898; hg19: chr13-93736849;