rs279929

Variant names:

• chr13-103088369-T-C
• rs279929

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.425 AC: 17609 AN: 41470

American (AMR) AF: 0.382 AC: 5834 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.204 AC: 706 AN: 3468

East Asian (EAS) AF: 0.333 AC: 1725 AN: 5182

South Asian (SAS) AF: 0.295 AC: 1425 AN: 4826

European-Finnish (FIN) AF: 0.260 AC: 2756 AN: 10580

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.271 AC: 18391 AN: 67970

Other (OTH) AF: 0.286 AC: 603 AN: 2110

Alfa AF: 0.293 Hom.: 3994

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
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs279929; hg19: chr13-103740719;