6-129711600-T-C

Variant names:

• chr6-129711600-T-C
• rs12213388

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 0.17 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
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• 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

African (AFR) AF: 0.217 AC: 9000 AN: 41492

American (AMR) AF: 0.213 AC: 3256 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.120 AC: 415 AN: 3470

East Asian (EAS) AF: 0.0826 AC: 428 AN: 5184

South Asian (SAS) AF: 0.110 AC: 530 AN: 4826

European-Finnish (FIN) AF: 0.0930 AC: 985 AN: 10590

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.157 AC: 10690 AN: 67974

Other (OTH) AF: 0.181 AC: 381 AN: 2110

Alfa AF: 0.160 Hom.: 1625

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
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs12213388; hg19: chr6-130032745;