rs13098270

Variant names:

• chr3-88898198-C-T
• rs13098270

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 0.131 in 152,106 control chromosomes in the GnomAD database, including 1,489 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 0.13 (1489 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00900

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 (NFE) allele frequency at 95% confidence interval = 0.174 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: 0.131 AC: 19932 AN: 151988 Hom.: 1488 Cov.: 32

Gnomad AFR AF: 0.0667

Gnomad AMI AF: 0.0526

Gnomad AMR AF: 0.109

Gnomad ASJ AF: 0.148

Gnomad EAS AF: 0.172

Gnomad SAS AF: 0.0673

Gnomad FIN AF: 0.133

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.177

Gnomad OTH AF: 0.137

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

GnomAD4 genome AF: 0.131 AC: 19931 AN: 152106 Hom.: 1489 Cov.: 32 AF XY: 0.128 AC XY: 9526 AN XY: 74354

Gnomad4 AFR AF: 0.0666

Gnomad4 AMR AF: 0.109

Gnomad4 ASJ AF: 0.148

Gnomad4 EAS AF: 0.172

Gnomad4 SAS AF: 0.0665

Gnomad4 FIN AF: 0.133

Gnomad4 NFE AF: 0.177

Gnomad4 OTH AF: 0.140

Alfa AF: 0.160 Hom.: 260

Bravo AF: 0.126

Asia WGS AF: 0.116 AC: 404 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	1.1
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13098270; hg19: chr3-88947348;