rs12506209

Variant names:

• chr4-69876347-C-T
• rs12506209

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 0.333 in 151,642 control chromosomes in the GnomAD database, including 8,767 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 0.33 (8767 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.336
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.36 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: 0.334 AC: 50546 AN: 151524 Hom.: 8764 Cov.: 31

Gnomad AFR AF: 0.256

Gnomad AMI AF: 0.202

Gnomad AMR AF: 0.347

Gnomad ASJ AF: 0.484

Gnomad EAS AF: 0.312

Gnomad SAS AF: 0.375

Gnomad FIN AF: 0.426

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.354

Gnomad OTH AF: 0.363

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

GnomAD4 genome AF: 0.333 AC: 50567 AN: 151642 Hom.: 8767 Cov.: 31 AF XY: 0.338 AC XY: 25022 AN XY: 74090

African (AFR) AF: 0.256 AC: 10607 AN: 41374

American (AMR) AF: 0.347 AC: 5279 AN: 15204

Ashkenazi Jewish (ASJ) AF: 0.484 AC: 1677 AN: 3466

East Asian (EAS) AF: 0.311 AC: 1595 AN: 5122

South Asian (SAS) AF: 0.375 AC: 1807 AN: 4822

European-Finnish (FIN) AF: 0.426 AC: 4478 AN: 10516

Middle Eastern (MID) AF: 0.500 AC: 147 AN: 294

European-Non Finnish (NFE) AF: 0.354 AC: 24028 AN: 67822

Other (OTH) AF: 0.362 AC: 765 AN: 2112

Alfa AF: 0.316 Hom.: 1404

Bravo AF: 0.324

Asia WGS AF: 0.331 AC: 1152 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.3
DANN	Benign	0.74
PhyloP100		0.34

Splicing

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

Other links and lift over

dbSNP: rs12506209; hg19: chr4-70742065;