rs279929

Variant names:

• chr13-103088369-T-C
• rs279929

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 0.324 in 152,092 control chromosomes in the GnomAD database, including 8,517 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 0.32 (8517 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.285

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.419 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: 0.324 AC: 49293 AN: 151974 Hom.: 8503 Cov.: 33

Gnomad AFR AF: 0.425

Gnomad AMI AF: 0.247

Gnomad AMR AF: 0.381

Gnomad ASJ AF: 0.204

Gnomad EAS AF: 0.333

Gnomad SAS AF: 0.294

Gnomad FIN AF: 0.260

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.271

Gnomad OTH AF: 0.288

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

GnomAD4 genome AF: 0.324 AC: 49338 AN: 152092 Hom.: 8517 Cov.: 33 AF XY: 0.324 AC XY: 24116 AN XY: 74350

Gnomad4 AFR AF: 0.425

Gnomad4 AMR AF: 0.382

Gnomad4 ASJ AF: 0.204

Gnomad4 EAS AF: 0.333

Gnomad4 SAS AF: 0.295

Gnomad4 FIN AF: 0.260

Gnomad4 NFE AF: 0.271

Gnomad4 OTH AF: 0.286

Alfa AF: 0.293 Hom.: 3636

Bravo AF: 0.339

Asia WGS AF: 0.267 AC: 929 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.44
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs279929; hg19: chr13-103740719;