rs708356

Variant names:

• chr12-129989369-T-C
• rs708356

Your query was ambiguous. Multiple possible variants found:

• chr12-129989369-T-C
• chr12-129989369-T-G

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 0.364 in 151,832 control chromosomes in the GnomAD database, including 10,839 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 0.36 (10839 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.33

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.507 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: 0.364 AC: 55224 AN: 151714 Hom.: 10807 Cov.: 31

Gnomad AFR AF: 0.513

Gnomad AMI AF: 0.420

Gnomad AMR AF: 0.254

Gnomad ASJ AF: 0.301

Gnomad EAS AF: 0.247

Gnomad SAS AF: 0.369

Gnomad FIN AF: 0.291

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.322

Gnomad OTH AF: 0.319

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

GnomAD4 genome AF: 0.364 AC: 55306 AN: 151832 Hom.: 10839 Cov.: 31 AF XY: 0.358 AC XY: 26569 AN XY: 74194

Gnomad4 AFR AF: 0.513

Gnomad4 AMR AF: 0.254

Gnomad4 ASJ AF: 0.301

Gnomad4 EAS AF: 0.247

Gnomad4 SAS AF: 0.370

Gnomad4 FIN AF: 0.291

Gnomad4 NFE AF: 0.322

Gnomad4 OTH AF: 0.319

Alfa AF: 0.318 Hom.: 12948

Bravo AF: 0.363

Asia WGS AF: 0.342 AC: 1189 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.6
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs708356; hg19: chr12-130473914;