rs13207033

Positions:

• chr6-137644281-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 0.243 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;