rs12706860

Positions:

• chr7-128929972-C-G
• chr7-128929972-C-T

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 0.311 in 151,982 control chromosomes in the GnomAD database, including 7,751 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 0.31 (7751 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.317

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.365 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.311 AC: 47269 AN: 151864 Hom.: 7738 Cov.: 31

Gnomad AFR AF: 0.266

Gnomad AMI AF: 0.398

Gnomad AMR AF: 0.231

Gnomad ASJ AF: 0.336

Gnomad EAS AF: 0.378

Gnomad SAS AF: 0.349

Gnomad FIN AF: 0.357

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.340

Gnomad OTH AF: 0.294

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

GnomAD4 genome AF: 0.311 AC: 47308 AN: 151982 Hom.: 7751 Cov.: 31 AF XY: 0.313 AC XY: 23257 AN XY: 74272

Gnomad4 AFR AF: 0.266

Gnomad4 AMR AF: 0.230

Gnomad4 ASJ AF: 0.336

Gnomad4 EAS AF: 0.379

Gnomad4 SAS AF: 0.348

Gnomad4 FIN AF: 0.357

Gnomad4 NFE AF: 0.340

Gnomad4 OTH AF: 0.292

Alfa AF: 0.198 Hom.: 418

Bravo AF: 0.299

Asia WGS AF: 0.369 AC: 1280 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.8
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12706860; hg19: chr7-128570026;