chr6-129711600-T-C

Variant names:

• chr6-129711600-T-C
• rs12213388

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 0.17 in 152,134 control chromosomes in the GnomAD database, including 2,396 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 0.17 (2396 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.242

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.213 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: 0.170 AC: 25802 AN: 152016 Hom.: 2389 Cov.: 32

Gnomad AFR AF: 0.217

Gnomad AMI AF: 0.0923

Gnomad AMR AF: 0.213

Gnomad ASJ AF: 0.120

Gnomad EAS AF: 0.0824

Gnomad SAS AF: 0.109

Gnomad FIN AF: 0.0930

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.157

Gnomad OTH AF: 0.183

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

GnomAD4 genome AF: 0.170 AC: 25841 AN: 152134 Hom.: 2396 Cov.: 32 AF XY: 0.168 AC XY: 12516 AN XY: 74390

Gnomad4 AFR AF: 0.217

Gnomad4 AMR AF: 0.213

Gnomad4 ASJ AF: 0.120

Gnomad4 EAS AF: 0.0826

Gnomad4 SAS AF: 0.110

Gnomad4 FIN AF: 0.0930

Gnomad4 NFE AF: 0.157

Gnomad4 OTH AF: 0.181

Alfa AF: 0.160 Hom.: 1176

Bravo AF: 0.184

Asia WGS AF: 0.107 AC: 370 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.5
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12213388; hg19: chr6-130032745;