rs13207033

Variant names:

• chr6-137644281-G-A
• rs13207033

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 0.243 in 152,092 control chromosomes in the GnomAD database, including 4,700 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 0.24 (4700 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.266

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.284 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: 0.243 AC: 36893 AN: 151974 Hom.: 4696 Cov.: 32

Gnomad AFR AF: 0.189

Gnomad AMI AF: 0.400

Gnomad AMR AF: 0.291

Gnomad ASJ AF: 0.342

Gnomad EAS AF: 0.0967

Gnomad SAS AF: 0.256

Gnomad FIN AF: 0.224

Gnomad MID AF: 0.290

Gnomad NFE AF: 0.271

Gnomad OTH AF: 0.246

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

GnomAD4 genome AF: 0.243 AC: 36897 AN: 152092 Hom.: 4700 Cov.: 32 AF XY: 0.241 AC XY: 17955 AN XY: 74364

Gnomad4 AFR AF: 0.188

Gnomad4 AMR AF: 0.291

Gnomad4 ASJ AF: 0.342

Gnomad4 EAS AF: 0.0966

Gnomad4 SAS AF: 0.257

Gnomad4 FIN AF: 0.224

Gnomad4 NFE AF: 0.271

Gnomad4 OTH AF: 0.244

Alfa AF: 0.276 Hom.: 5965

Bravo AF: 0.248

Asia WGS AF: 0.156 AC: 545 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	6.5
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13207033; hg19: chr6-137965418;