rs13207033

Variant names:

• chr6-137644281-G-A
• rs13207033

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 0.243 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
• Publications: 38 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.188 AC: 7803 AN: 41486

American (AMR) AF: 0.291 AC: 4448 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.342 AC: 1187 AN: 3470

East Asian (EAS) AF: 0.0966 AC: 501 AN: 5188

South Asian (SAS) AF: 0.257 AC: 1237 AN: 4818

European-Finnish (FIN) AF: 0.224 AC: 2365 AN: 10562

Middle Eastern (MID) AF: 0.277 AC: 81 AN: 292

European-Non Finnish (NFE) AF: 0.271 AC: 18393 AN: 67954

Other (OTH) AF: 0.244 AC: 517 AN: 2116

Alfa AF: 0.274 Hom.: 7100

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
PhyloP100		0.27

Splicing

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

Other links and lift over

dbSNP: rs13207033; hg19: chr6-137965418;