rs282606

chr13-112685447-G-A

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 0.249 in 152,096 control chromosomes in the GnomAD database, including 7,174 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 (7174 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.20

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.53 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.249 AC: 37788 AN: 151978 Hom.: 7144 Cov.: 32

Gnomad AFR AF: 0.536

Gnomad AMI AF: 0.137

Gnomad AMR AF: 0.206

Gnomad ASJ AF: 0.145

Gnomad EAS AF: 0.0762

Gnomad SAS AF: 0.0886

Gnomad FIN AF: 0.131

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.135

Gnomad OTH AF: 0.214

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

GnomAD4 genome AF: 0.249 AC: 37870 AN: 152096 Hom.: 7174 Cov.: 32 AF XY: 0.244 AC XY: 18179 AN XY: 74360

Gnomad4 AFR AF: 0.536

Gnomad4 AMR AF: 0.207

Gnomad4 ASJ AF: 0.145

Gnomad4 EAS AF: 0.0762

Gnomad4 SAS AF: 0.0874

Gnomad4 FIN AF: 0.131

Gnomad4 NFE AF: 0.135

Gnomad4 OTH AF: 0.213

Alfa AF: 0.146 Hom.: 3968

Bravo AF: 0.268

Asia WGS AF: 0.121 AC: 421 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.47
Dann	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs282606; hg19: chr13-113339761;