rs12706860

Variant names:

• chr7-128929972-C-G
• rs12706860

Your query was ambiguous. Multiple possible variants found:

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

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 0.311 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
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.266 AC: 11039 AN: 41434

American (AMR) AF: 0.230 AC: 3520 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.336 AC: 1166 AN: 3472

East Asian (EAS) AF: 0.379 AC: 1952 AN: 5156

South Asian (SAS) AF: 0.348 AC: 1674 AN: 4808

European-Finnish (FIN) AF: 0.357 AC: 3770 AN: 10556

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.340 AC: 23126 AN: 67960

Other (OTH) AF: 0.292 AC: 614 AN: 2106

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
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs12706860; hg19: chr7-128570026;