13-28798306-A-G

Variant names:

• chr13-28798306-A-G
• rs952648

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 0.253 in 152,230 control chromosomes in the GnomAD database, including 5,565 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 0.25 (5565 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.696

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.377 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: 0.253 AC: 38505 AN: 152112 Hom.: 5560 Cov.: 32

Gnomad AFR AF: 0.126

Gnomad AMI AF: 0.166

Gnomad AMR AF: 0.346

Gnomad ASJ AF: 0.255

Gnomad EAS AF: 0.391

Gnomad SAS AF: 0.193

Gnomad FIN AF: 0.299

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.298

Gnomad OTH AF: 0.247

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

GnomAD4 genome AF: 0.253 AC: 38520 AN: 152230 Hom.: 5565 Cov.: 32 AF XY: 0.258 AC XY: 19238 AN XY: 74444

Gnomad4 AFR AF: 0.125

Gnomad4 AMR AF: 0.347

Gnomad4 ASJ AF: 0.255

Gnomad4 EAS AF: 0.391

Gnomad4 SAS AF: 0.192

Gnomad4 FIN AF: 0.299

Gnomad4 NFE AF: 0.297

Gnomad4 OTH AF: 0.247

Alfa AF: 0.292 Hom.: 13877

Bravo AF: 0.254

Asia WGS AF: 0.257 AC: 897 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.0
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs952648; hg19: chr13-29372443;