rs12706933

Variant names:

• chr7-130468307-G-A
• rs12706933

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 0.319 in 151,620 control chromosomes in the GnomAD database, including 9,557 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 0.32 (9557 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.03
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.605 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: 0.319 AC: 48277 AN: 151500 Hom.: 9544 Cov.: 31

Gnomad AFR AF: 0.0866

Gnomad AMI AF: 0.440

Gnomad AMR AF: 0.467

Gnomad ASJ AF: 0.425

Gnomad EAS AF: 0.624

Gnomad SAS AF: 0.536

Gnomad FIN AF: 0.344

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.375

Gnomad OTH AF: 0.364

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

GnomAD4 genome AF: 0.319 AC: 48301 AN: 151620 Hom.: 9557 Cov.: 31 AF XY: 0.326 AC XY: 24176 AN XY: 74104

African (AFR) AF: 0.0865 AC: 3564 AN: 41224

American (AMR) AF: 0.468 AC: 7121 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.425 AC: 1477 AN: 3472

East Asian (EAS) AF: 0.623 AC: 3218 AN: 5162

South Asian (SAS) AF: 0.537 AC: 2571 AN: 4790

European-Finnish (FIN) AF: 0.344 AC: 3609 AN: 10498

Middle Eastern (MID) AF: 0.364 AC: 107 AN: 294

European-Non Finnish (NFE) AF: 0.375 AC: 25458 AN: 67936

Other (OTH) AF: 0.369 AC: 776 AN: 2102

Alfa AF: 0.372 Hom.: 7738

Bravo AF: 0.319

Asia WGS AF: 0.605 AC: 2098 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	7.7
DANN	Benign	0.82
PhyloP100		1.0

Splicing

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

Other links and lift over

dbSNP: rs12706933; hg19: chr7-130108148;