rs282606

Variant names:

• chr13-112685447-G-A
• rs282606

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 0.249 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
• Publications: 15 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.536 AC: 22209 AN: 41428

American (AMR) AF: 0.207 AC: 3157 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.145 AC: 504 AN: 3472

East Asian (EAS) AF: 0.0762 AC: 395 AN: 5186

South Asian (SAS) AF: 0.0874 AC: 421 AN: 4816

European-Finnish (FIN) AF: 0.131 AC: 1387 AN: 10596

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

European-Non Finnish (NFE) AF: 0.135 AC: 9159 AN: 68004

Other (OTH) AF: 0.213 AC: 449 AN: 2112

Alfa AF: 0.168 Hom.: 12739

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
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs282606; hg19: chr13-113339761;